@bgicli/bgicli 2.1.1 → 2.2.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (1267) hide show
  1. package/README.md +152 -74
  2. package/data/skills/aav-vector-design-agent/SKILL.md +198 -0
  3. package/data/skills/adaptyv/SKILL.md +112 -0
  4. package/data/skills/adhd-daily-planner/SKILL.md +271 -0
  5. package/data/skills/aeon/SKILL.md +372 -0
  6. package/data/skills/agent-browser/SKILL.md +159 -0
  7. package/data/skills/agentd-drug-discovery/SKILL.md +52 -0
  8. package/data/skills/ai-analyzer/SKILL.md +218 -0
  9. package/data/skills/alphafold/SKILL.md +183 -0
  10. package/data/skills/alphafold-database/SKILL.md +500 -0
  11. package/data/skills/anndata/SKILL.md +394 -0
  12. package/data/skills/antibody-design-agent/SKILL.md +64 -0
  13. package/data/skills/arboreto/SKILL.md +237 -0
  14. package/data/skills/armored-cart-design-agent/SKILL.md +225 -0
  15. package/data/skills/arxiv-search/SKILL.md +224 -0
  16. package/data/skills/autonomous-oncology-agent/SKILL.md +77 -0
  17. package/data/skills/bayesian-optimizer/SKILL.md +60 -0
  18. package/data/skills/benchling-integration/SKILL.md +473 -0
  19. package/data/skills/bgpt-paper-search/SKILL.md +81 -0
  20. package/data/skills/bindcraft/SKILL.md +198 -0
  21. package/data/skills/binder-design/SKILL.md +182 -0
  22. package/data/skills/binding-characterization/SKILL.md +234 -0
  23. package/data/skills/bindingdb-database/SKILL.md +332 -0
  24. package/data/skills/bio-admet-prediction/SKILL.md +224 -0
  25. package/data/skills/bio-alignment-files-bam-statistics/SKILL.md +340 -0
  26. package/data/skills/bio-alignment-filtering/SKILL.md +322 -0
  27. package/data/skills/bio-alignment-indexing/SKILL.md +249 -0
  28. package/data/skills/bio-alignment-io/SKILL.md +301 -0
  29. package/data/skills/bio-alignment-msa-parsing/SKILL.md +366 -0
  30. package/data/skills/bio-alignment-msa-statistics/SKILL.md +375 -0
  31. package/data/skills/bio-alignment-pairwise/SKILL.md +277 -0
  32. package/data/skills/bio-alignment-sorting/SKILL.md +296 -0
  33. package/data/skills/bio-alignment-validation/SKILL.md +374 -0
  34. package/data/skills/bio-atac-seq-atac-peak-calling/SKILL.md +221 -0
  35. package/data/skills/bio-atac-seq-atac-qc/SKILL.md +292 -0
  36. package/data/skills/bio-atac-seq-differential-accessibility/SKILL.md +268 -0
  37. package/data/skills/bio-atac-seq-footprinting/SKILL.md +256 -0
  38. package/data/skills/bio-atac-seq-motif-deviation/SKILL.md +319 -0
  39. package/data/skills/bio-atac-seq-nucleosome-positioning/SKILL.md +321 -0
  40. package/data/skills/bio-basecalling/SKILL.md +368 -0
  41. package/data/skills/bio-batch-downloads/SKILL.md +384 -0
  42. package/data/skills/bio-batch-processing/SKILL.md +303 -0
  43. package/data/skills/bio-bedgraph-handling/SKILL.md +336 -0
  44. package/data/skills/bio-blast-searches/SKILL.md +354 -0
  45. package/data/skills/bio-causal-genomics-colocalization-analysis/SKILL.md +264 -0
  46. package/data/skills/bio-causal-genomics-fine-mapping/SKILL.md +267 -0
  47. package/data/skills/bio-causal-genomics-mediation-analysis/SKILL.md +264 -0
  48. package/data/skills/bio-causal-genomics-mendelian-randomization/SKILL.md +221 -0
  49. package/data/skills/bio-causal-genomics-pleiotropy-detection/SKILL.md +292 -0
  50. package/data/skills/bio-cfdna-preprocessing/SKILL.md +200 -0
  51. package/data/skills/bio-chipseq-differential-binding/SKILL.md +262 -0
  52. package/data/skills/bio-chipseq-motif-analysis/SKILL.md +387 -0
  53. package/data/skills/bio-chipseq-peak-annotation/SKILL.md +239 -0
  54. package/data/skills/bio-chipseq-peak-calling/SKILL.md +277 -0
  55. package/data/skills/bio-chipseq-qc/SKILL.md +391 -0
  56. package/data/skills/bio-chipseq-super-enhancers/SKILL.md +288 -0
  57. package/data/skills/bio-chipseq-visualization/SKILL.md +289 -0
  58. package/data/skills/bio-clinical-databases-clinvar-lookup/SKILL.md +188 -0
  59. package/data/skills/bio-clinical-databases-dbsnp-queries/SKILL.md +171 -0
  60. package/data/skills/bio-clinical-databases-gnomad-frequencies/SKILL.md +205 -0
  61. package/data/skills/bio-clinical-databases-hla-typing/SKILL.md +248 -0
  62. package/data/skills/bio-clinical-databases-myvariant-queries/SKILL.md +174 -0
  63. package/data/skills/bio-clinical-databases-pharmacogenomics/SKILL.md +232 -0
  64. package/data/skills/bio-clinical-databases-polygenic-risk/SKILL.md +276 -0
  65. package/data/skills/bio-clinical-databases-somatic-signatures/SKILL.md +261 -0
  66. package/data/skills/bio-clinical-databases-tumor-mutational-burden/SKILL.md +301 -0
  67. package/data/skills/bio-clinical-databases-variant-prioritization/SKILL.md +225 -0
  68. package/data/skills/bio-clip-seq-binding-site-annotation/SKILL.md +66 -0
  69. package/data/skills/bio-clip-seq-clip-alignment/SKILL.md +70 -0
  70. package/data/skills/bio-clip-seq-clip-motif-analysis/SKILL.md +62 -0
  71. package/data/skills/bio-clip-seq-clip-peak-calling/SKILL.md +282 -0
  72. package/data/skills/bio-clip-seq-clip-preprocessing/SKILL.md +142 -0
  73. package/data/skills/bio-codon-usage/SKILL.md +353 -0
  74. package/data/skills/bio-comparative-genomics-ancestral-reconstruction/SKILL.md +312 -0
  75. package/data/skills/bio-comparative-genomics-hgt-detection/SKILL.md +341 -0
  76. package/data/skills/bio-comparative-genomics-ortholog-inference/SKILL.md +308 -0
  77. package/data/skills/bio-comparative-genomics-positive-selection/SKILL.md +354 -0
  78. package/data/skills/bio-comparative-genomics-synteny-analysis/SKILL.md +315 -0
  79. package/data/skills/bio-compressed-files/SKILL.md +263 -0
  80. package/data/skills/bio-consensus-sequences/SKILL.md +340 -0
  81. package/data/skills/bio-copy-number-cnv-annotation/SKILL.md +307 -0
  82. package/data/skills/bio-copy-number-cnv-visualization/SKILL.md +294 -0
  83. package/data/skills/bio-copy-number-cnvkit-analysis/SKILL.md +290 -0
  84. package/data/skills/bio-copy-number-gatk-cnv/SKILL.md +270 -0
  85. package/data/skills/bio-crispr-screens-base-editing-analysis/SKILL.md +110 -0
  86. package/data/skills/bio-crispr-screens-batch-correction/SKILL.md +316 -0
  87. package/data/skills/bio-crispr-screens-crispresso-editing/SKILL.md +205 -0
  88. package/data/skills/bio-crispr-screens-hit-calling/SKILL.md +264 -0
  89. package/data/skills/bio-crispr-screens-jacks-analysis/SKILL.md +313 -0
  90. package/data/skills/bio-crispr-screens-library-design/SKILL.md +417 -0
  91. package/data/skills/bio-crispr-screens-mageck-analysis/SKILL.md +222 -0
  92. package/data/skills/bio-crispr-screens-screen-qc/SKILL.md +243 -0
  93. package/data/skills/bio-ctdna-mutation-detection/SKILL.md +234 -0
  94. package/data/skills/bio-data-visualization-circos-plots/SKILL.md +405 -0
  95. package/data/skills/bio-data-visualization-color-palettes/SKILL.md +244 -0
  96. package/data/skills/bio-data-visualization-genome-browser-tracks/SKILL.md +328 -0
  97. package/data/skills/bio-data-visualization-genome-tracks/SKILL.md +249 -0
  98. package/data/skills/bio-data-visualization-ggplot2-fundamentals/SKILL.md +313 -0
  99. package/data/skills/bio-data-visualization-heatmaps-clustering/SKILL.md +227 -0
  100. package/data/skills/bio-data-visualization-interactive-visualization/SKILL.md +210 -0
  101. package/data/skills/bio-data-visualization-multipanel-figures/SKILL.md +274 -0
  102. package/data/skills/bio-data-visualization-specialized-omics-plots/SKILL.md +251 -0
  103. package/data/skills/bio-data-visualization-upset-plots/SKILL.md +228 -0
  104. package/data/skills/bio-data-visualization-volcano-customization/SKILL.md +233 -0
  105. package/data/skills/bio-de-deseq2-basics/SKILL.md +376 -0
  106. package/data/skills/bio-de-edger-basics/SKILL.md +418 -0
  107. package/data/skills/bio-de-results/SKILL.md +378 -0
  108. package/data/skills/bio-de-visualization/SKILL.md +408 -0
  109. package/data/skills/bio-differential-expression-batch-correction/SKILL.md +253 -0
  110. package/data/skills/bio-differential-expression-timeseries-de/SKILL.md +370 -0
  111. package/data/skills/bio-differential-splicing/SKILL.md +177 -0
  112. package/data/skills/bio-duplicate-handling/SKILL.md +292 -0
  113. package/data/skills/bio-entrez-fetch/SKILL.md +334 -0
  114. package/data/skills/bio-entrez-link/SKILL.md +325 -0
  115. package/data/skills/bio-entrez-search/SKILL.md +311 -0
  116. package/data/skills/bio-epidemiological-genomics-amr-surveillance/SKILL.md +233 -0
  117. package/data/skills/bio-epidemiological-genomics-pathogen-typing/SKILL.md +202 -0
  118. package/data/skills/bio-epidemiological-genomics-phylodynamics/SKILL.md +207 -0
  119. package/data/skills/bio-epidemiological-genomics-transmission-inference/SKILL.md +237 -0
  120. package/data/skills/bio-epidemiological-genomics-variant-surveillance/SKILL.md +237 -0
  121. package/data/skills/bio-epitranscriptomics-m6a-differential/SKILL.md +88 -0
  122. package/data/skills/bio-epitranscriptomics-m6a-peak-calling/SKILL.md +89 -0
  123. package/data/skills/bio-epitranscriptomics-m6anet-analysis/SKILL.md +101 -0
  124. package/data/skills/bio-epitranscriptomics-merip-preprocessing/SKILL.md +81 -0
  125. package/data/skills/bio-epitranscriptomics-modification-visualization/SKILL.md +98 -0
  126. package/data/skills/bio-experimental-design-batch-design/SKILL.md +110 -0
  127. package/data/skills/bio-experimental-design-multiple-testing/SKILL.md +98 -0
  128. package/data/skills/bio-experimental-design-power-analysis/SKILL.md +84 -0
  129. package/data/skills/bio-experimental-design-sample-size/SKILL.md +93 -0
  130. package/data/skills/bio-expression-matrix-counts-ingest/SKILL.md +220 -0
  131. package/data/skills/bio-expression-matrix-gene-id-mapping/SKILL.md +256 -0
  132. package/data/skills/bio-expression-matrix-metadata-joins/SKILL.md +271 -0
  133. package/data/skills/bio-expression-matrix-sparse-handling/SKILL.md +247 -0
  134. package/data/skills/bio-fastq-quality/SKILL.md +279 -0
  135. package/data/skills/bio-filter-sequences/SKILL.md +265 -0
  136. package/data/skills/bio-flow-cytometry-bead-normalization/SKILL.md +315 -0
  137. package/data/skills/bio-flow-cytometry-clustering-phenotyping/SKILL.md +237 -0
  138. package/data/skills/bio-flow-cytometry-compensation-transformation/SKILL.md +196 -0
  139. package/data/skills/bio-flow-cytometry-cytometry-qc/SKILL.md +382 -0
  140. package/data/skills/bio-flow-cytometry-differential-analysis/SKILL.md +217 -0
  141. package/data/skills/bio-flow-cytometry-doublet-detection/SKILL.md +288 -0
  142. package/data/skills/bio-flow-cytometry-fcs-handling/SKILL.md +221 -0
  143. package/data/skills/bio-flow-cytometry-gating-analysis/SKILL.md +193 -0
  144. package/data/skills/bio-format-conversion/SKILL.md +193 -0
  145. package/data/skills/bio-fragment-analysis/SKILL.md +214 -0
  146. package/data/skills/bio-gatk-variant-calling/SKILL.md +422 -0
  147. package/data/skills/bio-genome-assembly-assembly-polishing/SKILL.md +333 -0
  148. package/data/skills/bio-genome-assembly-assembly-qc/SKILL.md +344 -0
  149. package/data/skills/bio-genome-assembly-contamination-detection/SKILL.md +235 -0
  150. package/data/skills/bio-genome-assembly-hifi-assembly/SKILL.md +178 -0
  151. package/data/skills/bio-genome-assembly-long-read-assembly/SKILL.md +307 -0
  152. package/data/skills/bio-genome-assembly-metagenome-assembly/SKILL.md +227 -0
  153. package/data/skills/bio-genome-assembly-scaffolding/SKILL.md +204 -0
  154. package/data/skills/bio-genome-assembly-short-read-assembly/SKILL.md +319 -0
  155. package/data/skills/bio-genome-engineering-base-editing-design/SKILL.md +277 -0
  156. package/data/skills/bio-genome-engineering-grna-design/SKILL.md +221 -0
  157. package/data/skills/bio-genome-engineering-hdr-template-design/SKILL.md +264 -0
  158. package/data/skills/bio-genome-engineering-off-target-prediction/SKILL.md +232 -0
  159. package/data/skills/bio-genome-engineering-prime-editing-design/SKILL.md +275 -0
  160. package/data/skills/bio-genome-intervals-bed-file-basics/SKILL.md +357 -0
  161. package/data/skills/bio-genome-intervals-bigwig-tracks/SKILL.md +351 -0
  162. package/data/skills/bio-genome-intervals-coverage-analysis/SKILL.md +300 -0
  163. package/data/skills/bio-genome-intervals-gtf-gff-handling/SKILL.md +345 -0
  164. package/data/skills/bio-genome-intervals-interval-arithmetic/SKILL.md +485 -0
  165. package/data/skills/bio-genome-intervals-proximity-operations/SKILL.md +337 -0
  166. package/data/skills/bio-geo-data/SKILL.md +380 -0
  167. package/data/skills/bio-hi-c-analysis-compartment-analysis/SKILL.md +261 -0
  168. package/data/skills/bio-hi-c-analysis-contact-pairs/SKILL.md +278 -0
  169. package/data/skills/bio-hi-c-analysis-hic-data-io/SKILL.md +260 -0
  170. package/data/skills/bio-hi-c-analysis-hic-differential/SKILL.md +328 -0
  171. package/data/skills/bio-hi-c-analysis-hic-visualization/SKILL.md +297 -0
  172. package/data/skills/bio-hi-c-analysis-loop-calling/SKILL.md +284 -0
  173. package/data/skills/bio-hi-c-analysis-matrix-operations/SKILL.md +274 -0
  174. package/data/skills/bio-hi-c-analysis-tad-detection/SKILL.md +239 -0
  175. package/data/skills/bio-imaging-mass-cytometry-cell-segmentation/SKILL.md +241 -0
  176. package/data/skills/bio-imaging-mass-cytometry-data-preprocessing/SKILL.md +279 -0
  177. package/data/skills/bio-imaging-mass-cytometry-interactive-annotation/SKILL.md +304 -0
  178. package/data/skills/bio-imaging-mass-cytometry-phenotyping/SKILL.md +231 -0
  179. package/data/skills/bio-imaging-mass-cytometry-quality-metrics/SKILL.md +316 -0
  180. package/data/skills/bio-imaging-mass-cytometry-spatial-analysis/SKILL.md +246 -0
  181. package/data/skills/bio-immunoinformatics-epitope-prediction/SKILL.md +259 -0
  182. package/data/skills/bio-immunoinformatics-immunogenicity-scoring/SKILL.md +275 -0
  183. package/data/skills/bio-immunoinformatics-mhc-binding-prediction/SKILL.md +260 -0
  184. package/data/skills/bio-immunoinformatics-neoantigen-prediction/SKILL.md +277 -0
  185. package/data/skills/bio-immunoinformatics-tcr-epitope-binding/SKILL.md +257 -0
  186. package/data/skills/bio-isoform-switching/SKILL.md +192 -0
  187. package/data/skills/bio-liquid-biopsy-pipeline/SKILL.md +311 -0
  188. package/data/skills/bio-local-blast/SKILL.md +350 -0
  189. package/data/skills/bio-long-read-sequencing-clair3-variants/SKILL.md +252 -0
  190. package/data/skills/bio-long-read-sequencing-isoseq-analysis/SKILL.md +334 -0
  191. package/data/skills/bio-long-read-sequencing-nanopore-methylation/SKILL.md +110 -0
  192. package/data/skills/bio-longitudinal-monitoring/SKILL.md +271 -0
  193. package/data/skills/bio-longread-alignment/SKILL.md +193 -0
  194. package/data/skills/bio-longread-medaka/SKILL.md +176 -0
  195. package/data/skills/bio-longread-qc/SKILL.md +224 -0
  196. package/data/skills/bio-longread-structural-variants/SKILL.md +201 -0
  197. package/data/skills/bio-machine-learning-atlas-mapping/SKILL.md +139 -0
  198. package/data/skills/bio-machine-learning-biomarker-discovery/SKILL.md +157 -0
  199. package/data/skills/bio-machine-learning-model-validation/SKILL.md +148 -0
  200. package/data/skills/bio-machine-learning-omics-classifiers/SKILL.md +146 -0
  201. package/data/skills/bio-machine-learning-prediction-explanation/SKILL.md +162 -0
  202. package/data/skills/bio-machine-learning-survival-analysis/SKILL.md +176 -0
  203. package/data/skills/bio-metabolomics-lipidomics/SKILL.md +265 -0
  204. package/data/skills/bio-metabolomics-metabolite-annotation/SKILL.md +241 -0
  205. package/data/skills/bio-metabolomics-msdial-preprocessing/SKILL.md +308 -0
  206. package/data/skills/bio-metabolomics-normalization-qc/SKILL.md +283 -0
  207. package/data/skills/bio-metabolomics-pathway-mapping/SKILL.md +237 -0
  208. package/data/skills/bio-metabolomics-statistical-analysis/SKILL.md +276 -0
  209. package/data/skills/bio-metabolomics-targeted-analysis/SKILL.md +314 -0
  210. package/data/skills/bio-metabolomics-xcms-preprocessing/SKILL.md +268 -0
  211. package/data/skills/bio-metagenomics-abundance/SKILL.md +203 -0
  212. package/data/skills/bio-metagenomics-amr-detection/SKILL.md +293 -0
  213. package/data/skills/bio-metagenomics-functional-profiling/SKILL.md +252 -0
  214. package/data/skills/bio-metagenomics-kraken/SKILL.md +204 -0
  215. package/data/skills/bio-metagenomics-metaphlan/SKILL.md +214 -0
  216. package/data/skills/bio-metagenomics-strain-tracking/SKILL.md +292 -0
  217. package/data/skills/bio-metagenomics-visualization/SKILL.md +240 -0
  218. package/data/skills/bio-methylation-based-detection/SKILL.md +223 -0
  219. package/data/skills/bio-methylation-bismark-alignment/SKILL.md +195 -0
  220. package/data/skills/bio-methylation-calling/SKILL.md +200 -0
  221. package/data/skills/bio-methylation-dmr-detection/SKILL.md +211 -0
  222. package/data/skills/bio-methylation-methylkit/SKILL.md +219 -0
  223. package/data/skills/bio-microbiome-amplicon-processing/SKILL.md +137 -0
  224. package/data/skills/bio-microbiome-differential-abundance/SKILL.md +147 -0
  225. package/data/skills/bio-microbiome-diversity-analysis/SKILL.md +188 -0
  226. package/data/skills/bio-microbiome-functional-prediction/SKILL.md +153 -0
  227. package/data/skills/bio-microbiome-qiime2-workflow/SKILL.md +219 -0
  228. package/data/skills/bio-microbiome-taxonomy-assignment/SKILL.md +168 -0
  229. package/data/skills/bio-molecular-descriptors/SKILL.md +200 -0
  230. package/data/skills/bio-molecular-io/SKILL.md +188 -0
  231. package/data/skills/bio-motif-search/SKILL.md +354 -0
  232. package/data/skills/bio-multi-omics-data-harmonization/SKILL.md +228 -0
  233. package/data/skills/bio-multi-omics-mixomics-analysis/SKILL.md +221 -0
  234. package/data/skills/bio-multi-omics-mofa-integration/SKILL.md +225 -0
  235. package/data/skills/bio-multi-omics-similarity-network/SKILL.md +235 -0
  236. package/data/skills/bio-orchestrator/SKILL.md +133 -0
  237. package/data/skills/bio-paired-end-fastq/SKILL.md +334 -0
  238. package/data/skills/bio-pathway-enrichment-visualization/SKILL.md +278 -0
  239. package/data/skills/bio-pathway-go-enrichment/SKILL.md +218 -0
  240. package/data/skills/bio-pathway-gsea/SKILL.md +227 -0
  241. package/data/skills/bio-pathway-kegg-pathways/SKILL.md +234 -0
  242. package/data/skills/bio-pathway-reactome/SKILL.md +215 -0
  243. package/data/skills/bio-pathway-wikipathways/SKILL.md +255 -0
  244. package/data/skills/bio-pdb-geometric-analysis/SKILL.md +475 -0
  245. package/data/skills/bio-pdb-structure-io/SKILL.md +296 -0
  246. package/data/skills/bio-pdb-structure-modification/SKILL.md +448 -0
  247. package/data/skills/bio-pdb-structure-navigation/SKILL.md +335 -0
  248. package/data/skills/bio-phasing-imputation-genotype-imputation/SKILL.md +201 -0
  249. package/data/skills/bio-phasing-imputation-haplotype-phasing/SKILL.md +190 -0
  250. package/data/skills/bio-phasing-imputation-imputation-qc/SKILL.md +265 -0
  251. package/data/skills/bio-phasing-imputation-reference-panels/SKILL.md +203 -0
  252. package/data/skills/bio-phylo-distance-calculations/SKILL.md +307 -0
  253. package/data/skills/bio-phylo-modern-tree-inference/SKILL.md +274 -0
  254. package/data/skills/bio-phylo-tree-io/SKILL.md +252 -0
  255. package/data/skills/bio-phylo-tree-manipulation/SKILL.md +375 -0
  256. package/data/skills/bio-phylo-tree-visualization/SKILL.md +275 -0
  257. package/data/skills/bio-pileup-generation/SKILL.md +314 -0
  258. package/data/skills/bio-population-genetics-association-testing/SKILL.md +293 -0
  259. package/data/skills/bio-population-genetics-linkage-disequilibrium/SKILL.md +260 -0
  260. package/data/skills/bio-population-genetics-plink-basics/SKILL.md +338 -0
  261. package/data/skills/bio-population-genetics-population-structure/SKILL.md +352 -0
  262. package/data/skills/bio-population-genetics-scikit-allel-analysis/SKILL.md +306 -0
  263. package/data/skills/bio-population-genetics-selection-statistics/SKILL.md +251 -0
  264. package/data/skills/bio-primer-design-primer-basics/SKILL.md +289 -0
  265. package/data/skills/bio-primer-design-primer-validation/SKILL.md +344 -0
  266. package/data/skills/bio-primer-design-qpcr-primers/SKILL.md +273 -0
  267. package/data/skills/bio-proteomics-data-import/SKILL.md +122 -0
  268. package/data/skills/bio-proteomics-dia-analysis/SKILL.md +246 -0
  269. package/data/skills/bio-proteomics-differential-abundance/SKILL.md +129 -0
  270. package/data/skills/bio-proteomics-peptide-identification/SKILL.md +122 -0
  271. package/data/skills/bio-proteomics-protein-inference/SKILL.md +174 -0
  272. package/data/skills/bio-proteomics-proteomics-qc/SKILL.md +208 -0
  273. package/data/skills/bio-proteomics-ptm-analysis/SKILL.md +139 -0
  274. package/data/skills/bio-proteomics-quantification/SKILL.md +141 -0
  275. package/data/skills/bio-proteomics-spectral-libraries/SKILL.md +270 -0
  276. package/data/skills/bio-reaction-enumeration/SKILL.md +251 -0
  277. package/data/skills/bio-read-alignment-bowtie2-alignment/SKILL.md +189 -0
  278. package/data/skills/bio-read-alignment-bwa-alignment/SKILL.md +166 -0
  279. package/data/skills/bio-read-alignment-hisat2-alignment/SKILL.md +205 -0
  280. package/data/skills/bio-read-alignment-star-alignment/SKILL.md +204 -0
  281. package/data/skills/bio-read-qc-adapter-trimming/SKILL.md +222 -0
  282. package/data/skills/bio-read-qc-contamination-screening/SKILL.md +252 -0
  283. package/data/skills/bio-read-qc-fastp-workflow/SKILL.md +278 -0
  284. package/data/skills/bio-read-qc-quality-filtering/SKILL.md +231 -0
  285. package/data/skills/bio-read-qc-quality-reports/SKILL.md +204 -0
  286. package/data/skills/bio-read-qc-umi-processing/SKILL.md +391 -0
  287. package/data/skills/bio-read-sequences/SKILL.md +319 -0
  288. package/data/skills/bio-reference-operations/SKILL.md +302 -0
  289. package/data/skills/bio-reporting-automated-qc-reports/SKILL.md +103 -0
  290. package/data/skills/bio-reporting-figure-export/SKILL.md +112 -0
  291. package/data/skills/bio-reporting-jupyter-reports/SKILL.md +98 -0
  292. package/data/skills/bio-reporting-quarto-reports/SKILL.md +295 -0
  293. package/data/skills/bio-reporting-rmarkdown-reports/SKILL.md +276 -0
  294. package/data/skills/bio-research-tools-biomarker-signature-studio/SKILL.md +99 -0
  295. package/data/skills/bio-restriction-enzyme-selection/SKILL.md +342 -0
  296. package/data/skills/bio-restriction-fragment-analysis/SKILL.md +259 -0
  297. package/data/skills/bio-restriction-mapping/SKILL.md +239 -0
  298. package/data/skills/bio-restriction-sites/SKILL.md +222 -0
  299. package/data/skills/bio-reverse-complement/SKILL.md +250 -0
  300. package/data/skills/bio-ribo-seq-orf-detection/SKILL.md +303 -0
  301. package/data/skills/bio-ribo-seq-riboseq-preprocessing/SKILL.md +176 -0
  302. package/data/skills/bio-ribo-seq-ribosome-periodicity/SKILL.md +182 -0
  303. package/data/skills/bio-ribo-seq-ribosome-stalling/SKILL.md +217 -0
  304. package/data/skills/bio-ribo-seq-translation-efficiency/SKILL.md +183 -0
  305. package/data/skills/bio-rna-quantification-alignment-free-quant/SKILL.md +226 -0
  306. package/data/skills/bio-rna-quantification-count-matrix-qc/SKILL.md +310 -0
  307. package/data/skills/bio-rna-quantification-featurecounts-counting/SKILL.md +190 -0
  308. package/data/skills/bio-rna-quantification-tximport-workflow/SKILL.md +240 -0
  309. package/data/skills/bio-rnaseq-qc/SKILL.md +320 -0
  310. package/data/skills/bio-sam-bam-basics/SKILL.md +248 -0
  311. package/data/skills/bio-sashimi-plots/SKILL.md +175 -0
  312. package/data/skills/bio-seq-objects/SKILL.md +240 -0
  313. package/data/skills/bio-sequence-properties/SKILL.md +397 -0
  314. package/data/skills/bio-sequence-similarity/SKILL.md +335 -0
  315. package/data/skills/bio-sequence-slicing/SKILL.md +232 -0
  316. package/data/skills/bio-sequence-statistics/SKILL.md +318 -0
  317. package/data/skills/bio-similarity-searching/SKILL.md +200 -0
  318. package/data/skills/bio-single-cell-batch-integration/SKILL.md +317 -0
  319. package/data/skills/bio-single-cell-cell-annotation/SKILL.md +259 -0
  320. package/data/skills/bio-single-cell-cell-communication/SKILL.md +257 -0
  321. package/data/skills/bio-single-cell-clustering/SKILL.md +330 -0
  322. package/data/skills/bio-single-cell-data-io/SKILL.md +315 -0
  323. package/data/skills/bio-single-cell-doublet-detection/SKILL.md +362 -0
  324. package/data/skills/bio-single-cell-lineage-tracing/SKILL.md +319 -0
  325. package/data/skills/bio-single-cell-markers-annotation/SKILL.md +317 -0
  326. package/data/skills/bio-single-cell-metabolite-communication/SKILL.md +258 -0
  327. package/data/skills/bio-single-cell-multimodal-integration/SKILL.md +242 -0
  328. package/data/skills/bio-single-cell-perturb-seq/SKILL.md +258 -0
  329. package/data/skills/bio-single-cell-preprocessing/SKILL.md +338 -0
  330. package/data/skills/bio-single-cell-scatac-analysis/SKILL.md +326 -0
  331. package/data/skills/bio-single-cell-splicing/SKILL.md +199 -0
  332. package/data/skills/bio-single-cell-trajectory-inference/SKILL.md +225 -0
  333. package/data/skills/bio-small-rna-seq-differential-mirna/SKILL.md +194 -0
  334. package/data/skills/bio-small-rna-seq-mirdeep2-analysis/SKILL.md +180 -0
  335. package/data/skills/bio-small-rna-seq-mirge3-analysis/SKILL.md +178 -0
  336. package/data/skills/bio-small-rna-seq-smrna-preprocessing/SKILL.md +174 -0
  337. package/data/skills/bio-small-rna-seq-target-prediction/SKILL.md +202 -0
  338. package/data/skills/bio-spatial-transcriptomics-image-analysis/SKILL.md +283 -0
  339. package/data/skills/bio-spatial-transcriptomics-spatial-communication/SKILL.md +299 -0
  340. package/data/skills/bio-spatial-transcriptomics-spatial-data-io/SKILL.md +272 -0
  341. package/data/skills/bio-spatial-transcriptomics-spatial-deconvolution/SKILL.md +314 -0
  342. package/data/skills/bio-spatial-transcriptomics-spatial-domains/SKILL.md +254 -0
  343. package/data/skills/bio-spatial-transcriptomics-spatial-multiomics/SKILL.md +181 -0
  344. package/data/skills/bio-spatial-transcriptomics-spatial-neighbors/SKILL.md +198 -0
  345. package/data/skills/bio-spatial-transcriptomics-spatial-preprocessing/SKILL.md +269 -0
  346. package/data/skills/bio-spatial-transcriptomics-spatial-proteomics/SKILL.md +124 -0
  347. package/data/skills/bio-spatial-transcriptomics-spatial-statistics/SKILL.md +237 -0
  348. package/data/skills/bio-spatial-transcriptomics-spatial-visualization/SKILL.md +287 -0
  349. package/data/skills/bio-splicing-pipeline/SKILL.md +253 -0
  350. package/data/skills/bio-splicing-qc/SKILL.md +190 -0
  351. package/data/skills/bio-splicing-quantification/SKILL.md +145 -0
  352. package/data/skills/bio-sra-data/SKILL.md +363 -0
  353. package/data/skills/bio-structural-biology-alphafold-predictions/SKILL.md +258 -0
  354. package/data/skills/bio-structural-biology-modern-structure-prediction/SKILL.md +346 -0
  355. package/data/skills/bio-substructure-search/SKILL.md +206 -0
  356. package/data/skills/bio-systems-biology-context-specific-models/SKILL.md +241 -0
  357. package/data/skills/bio-systems-biology-flux-balance-analysis/SKILL.md +206 -0
  358. package/data/skills/bio-systems-biology-gene-essentiality/SKILL.md +235 -0
  359. package/data/skills/bio-systems-biology-metabolic-reconstruction/SKILL.md +215 -0
  360. package/data/skills/bio-systems-biology-model-curation/SKILL.md +243 -0
  361. package/data/skills/bio-tcr-bcr-analysis-immcantation-analysis/SKILL.md +195 -0
  362. package/data/skills/bio-tcr-bcr-analysis-mixcr-analysis/SKILL.md +167 -0
  363. package/data/skills/bio-tcr-bcr-analysis-repertoire-visualization/SKILL.md +224 -0
  364. package/data/skills/bio-tcr-bcr-analysis-scirpy-analysis/SKILL.md +168 -0
  365. package/data/skills/bio-tcr-bcr-analysis-vdjtools-analysis/SKILL.md +188 -0
  366. package/data/skills/bio-transcription-translation/SKILL.md +237 -0
  367. package/data/skills/bio-tumor-fraction-estimation/SKILL.md +211 -0
  368. package/data/skills/bio-uniprot-access/SKILL.md +239 -0
  369. package/data/skills/bio-variant-annotation/SKILL.md +410 -0
  370. package/data/skills/bio-variant-calling/SKILL.md +266 -0
  371. package/data/skills/bio-variant-calling-clinical-interpretation/SKILL.md +355 -0
  372. package/data/skills/bio-variant-calling-deepvariant/SKILL.md +315 -0
  373. package/data/skills/bio-variant-calling-filtering-best-practices/SKILL.md +403 -0
  374. package/data/skills/bio-variant-calling-joint-calling/SKILL.md +338 -0
  375. package/data/skills/bio-variant-calling-structural-variant-calling/SKILL.md +253 -0
  376. package/data/skills/bio-variant-normalization/SKILL.md +325 -0
  377. package/data/skills/bio-vcf-basics/SKILL.md +342 -0
  378. package/data/skills/bio-vcf-manipulation/SKILL.md +429 -0
  379. package/data/skills/bio-vcf-statistics/SKILL.md +445 -0
  380. package/data/skills/bio-virtual-screening/SKILL.md +263 -0
  381. package/data/skills/bio-workflow-management-cwl-workflows/SKILL.md +433 -0
  382. package/data/skills/bio-workflow-management-nextflow-pipelines/SKILL.md +386 -0
  383. package/data/skills/bio-workflow-management-snakemake-workflows/SKILL.md +383 -0
  384. package/data/skills/bio-workflow-management-wdl-workflows/SKILL.md +500 -0
  385. package/data/skills/bio-workflows-atacseq-pipeline/SKILL.md +362 -0
  386. package/data/skills/bio-workflows-biomarker-pipeline/SKILL.md +272 -0
  387. package/data/skills/bio-workflows-chipseq-pipeline/SKILL.md +282 -0
  388. package/data/skills/bio-workflows-clip-pipeline/SKILL.md +268 -0
  389. package/data/skills/bio-workflows-cnv-pipeline/SKILL.md +324 -0
  390. package/data/skills/bio-workflows-crispr-editing-pipeline/SKILL.md +455 -0
  391. package/data/skills/bio-workflows-crispr-screen-pipeline/SKILL.md +278 -0
  392. package/data/skills/bio-workflows-cytometry-pipeline/SKILL.md +328 -0
  393. package/data/skills/bio-workflows-expression-to-pathways/SKILL.md +329 -0
  394. package/data/skills/bio-workflows-fastq-to-variants/SKILL.md +374 -0
  395. package/data/skills/bio-workflows-genome-assembly-pipeline/SKILL.md +290 -0
  396. package/data/skills/bio-workflows-gwas-pipeline/SKILL.md +323 -0
  397. package/data/skills/bio-workflows-hic-pipeline/SKILL.md +304 -0
  398. package/data/skills/bio-workflows-imc-pipeline/SKILL.md +304 -0
  399. package/data/skills/bio-workflows-longread-sv-pipeline/SKILL.md +281 -0
  400. package/data/skills/bio-workflows-merip-pipeline/SKILL.md +222 -0
  401. package/data/skills/bio-workflows-metabolic-modeling-pipeline/SKILL.md +408 -0
  402. package/data/skills/bio-workflows-metabolomics-pipeline/SKILL.md +297 -0
  403. package/data/skills/bio-workflows-metagenomics-pipeline/SKILL.md +283 -0
  404. package/data/skills/bio-workflows-methylation-pipeline/SKILL.md +274 -0
  405. package/data/skills/bio-workflows-microbiome-pipeline/SKILL.md +221 -0
  406. package/data/skills/bio-workflows-multi-omics-pipeline/SKILL.md +362 -0
  407. package/data/skills/bio-workflows-multiome-pipeline/SKILL.md +298 -0
  408. package/data/skills/bio-workflows-neoantigen-pipeline/SKILL.md +325 -0
  409. package/data/skills/bio-workflows-outbreak-pipeline/SKILL.md +341 -0
  410. package/data/skills/bio-workflows-proteomics-pipeline/SKILL.md +226 -0
  411. package/data/skills/bio-workflows-riboseq-pipeline/SKILL.md +94 -0
  412. package/data/skills/bio-workflows-rnaseq-to-de/SKILL.md +345 -0
  413. package/data/skills/bio-workflows-scrnaseq-pipeline/SKILL.md +354 -0
  414. package/data/skills/bio-workflows-smrna-pipeline/SKILL.md +86 -0
  415. package/data/skills/bio-workflows-somatic-variant-pipeline/SKILL.md +313 -0
  416. package/data/skills/bio-workflows-spatial-pipeline/SKILL.md +267 -0
  417. package/data/skills/bio-workflows-tcr-pipeline/SKILL.md +84 -0
  418. package/data/skills/bio-write-sequences/SKILL.md +205 -0
  419. package/data/skills/bioinformatics-singlecell/SKILL.md +143 -0
  420. package/data/skills/biokernel/SKILL.md +61 -0
  421. package/data/skills/biologist-analyst/SKILL.md +799 -0
  422. package/data/skills/biomaster-workflows/SKILL.md +55 -0
  423. package/data/skills/biomcp-server/SKILL.md +65 -0
  424. package/data/skills/biomedical-data-analysis/SKILL.md +56 -0
  425. package/data/skills/biomedical-search/SKILL.md +214 -0
  426. package/data/skills/biomni/SKILL.md +309 -0
  427. package/data/skills/biomni-general-agent/SKILL.md +43 -0
  428. package/data/skills/biomni-research-agent/SKILL.md +76 -0
  429. package/data/skills/biopython/SKILL.md +437 -0
  430. package/data/skills/biorxiv-database/SKILL.md +477 -0
  431. package/data/skills/bioservices/SKILL.md +355 -0
  432. package/data/skills/boltz/SKILL.md +188 -0
  433. package/data/skills/boltzgen/SKILL.md +287 -0
  434. package/data/skills/bone-marrow-ai-agent/SKILL.md +163 -0
  435. package/data/skills/brainstorming/SKILL.md +96 -0
  436. package/data/skills/brenda-database/SKILL.md +714 -0
  437. package/data/skills/bulk-combat-correction/SKILL.md +54 -0
  438. package/data/skills/bulk-deg-analysis/SKILL.md +61 -0
  439. package/data/skills/bulk-deseq2-analysis/SKILL.md +50 -0
  440. package/data/skills/bulk-stringdb-ppi/SKILL.md +49 -0
  441. package/data/skills/bulk-to-single-deconvolution/SKILL.md +50 -0
  442. package/data/skills/bulk-trajblend-interpolation/SKILL.md +52 -0
  443. package/data/skills/bulk-wgcna-analysis/SKILL.md +56 -0
  444. package/data/skills/cancer-metabolism-agent/SKILL.md +180 -0
  445. package/data/skills/care-coordination/SKILL.md +35 -0
  446. package/data/skills/cart-design-optimizer-agent/SKILL.md +162 -0
  447. package/data/skills/cbioportal-database/SKILL.md +367 -0
  448. package/data/skills/cell-free-expression/SKILL.md +291 -0
  449. package/data/skills/cellagent-annotation/SKILL.md +69 -0
  450. package/data/skills/cellfree-rna-agent/SKILL.md +182 -0
  451. package/data/skills/cellular-senescence-agent/SKILL.md +183 -0
  452. package/data/skills/cellxgene-census/SKILL.md +505 -0
  453. package/data/skills/chai/SKILL.md +272 -0
  454. package/data/skills/chatehr-clinician-assistant/SKILL.md +67 -0
  455. package/data/skills/chematagent-drug-discovery/SKILL.md +68 -0
  456. package/data/skills/chembl-database/SKILL.md +383 -0
  457. package/data/skills/chembl-search/SKILL.md +211 -0
  458. package/data/skills/chemcrow-drug-discovery/SKILL.md +61 -0
  459. package/data/skills/chemical-property-lookup/SKILL.md +42 -0
  460. package/data/skills/chemist-analyst/SKILL.md +1603 -0
  461. package/data/skills/chemistry-agent/SKILL.md +62 -0
  462. package/data/skills/chip-clonal-hematopoiesis-agent/SKILL.md +224 -0
  463. package/data/skills/chromosomal-instability-agent/SKILL.md +187 -0
  464. package/data/skills/citation-management/SKILL.md +1081 -0
  465. package/data/skills/claims-appeals/SKILL.md +35 -0
  466. package/data/skills/claw-ancestry-pca/SKILL.md +145 -0
  467. package/data/skills/claw-metagenomics/SKILL.md +238 -0
  468. package/data/skills/claw-semantic-sim/SKILL.md +151 -0
  469. package/data/skills/clinical-decision-support/SKILL.md +504 -0
  470. package/data/skills/clinical-diagnostic-reasoning/SKILL.md +222 -0
  471. package/data/skills/clinical-nlp-extractor/SKILL.md +59 -0
  472. package/data/skills/clinical-note-summarization/SKILL.md +52 -0
  473. package/data/skills/clinical-reports/SKILL.md +1127 -0
  474. package/data/skills/clinical-trial-protocol-skill/SKILL.md +508 -0
  475. package/data/skills/clinical-trials-search/SKILL.md +211 -0
  476. package/data/skills/clinicaltrials-database/SKILL.md +501 -0
  477. package/data/skills/clinpgx/SKILL.md +96 -0
  478. package/data/skills/clinpgx-database/SKILL.md +632 -0
  479. package/data/skills/clinvar-database/SKILL.md +356 -0
  480. package/data/skills/cnv-caller-agent/SKILL.md +171 -0
  481. package/data/skills/coagulation-thrombosis-agent/SKILL.md +141 -0
  482. package/data/skills/cobrapy/SKILL.md +457 -0
  483. package/data/skills/compbioagent-explorer/SKILL.md +67 -0
  484. package/data/skills/computational-pathology-agent/SKILL.md +72 -0
  485. package/data/skills/convergence-study/SKILL.md +98 -0
  486. package/data/skills/cosmic-database/SKILL.md +330 -0
  487. package/data/skills/crisis-detection-intervention-ai/SKILL.md +569 -0
  488. package/data/skills/crisis-response-protocol/SKILL.md +456 -0
  489. package/data/skills/crispr-guide-design/SKILL.md +72 -0
  490. package/data/skills/crispr-offtarget-predictor/SKILL.md +56 -0
  491. package/data/skills/cryoem-ai-drug-design-agent/SKILL.md +216 -0
  492. package/data/skills/ctdna-dynamics-mrd-agent/SKILL.md +206 -0
  493. package/data/skills/cytokine-storm-analysis-agent/SKILL.md +180 -0
  494. package/data/skills/dask/SKILL.md +454 -0
  495. package/data/skills/data-stats-analysis/SKILL.md +477 -0
  496. package/data/skills/data-transform/SKILL.md +576 -0
  497. package/data/skills/data-visualization-biomedical/SKILL.md +252 -0
  498. package/data/skills/data-visualization-expert/SKILL.md +72 -0
  499. package/data/skills/data-viz-plots/SKILL.md +461 -0
  500. package/data/skills/datacommons-client/SKILL.md +253 -0
  501. package/data/skills/datamol/SKILL.md +700 -0
  502. package/data/skills/deep-research/SKILL.md +111 -0
  503. package/data/skills/deep-research-swarm/SKILL.md +62 -0
  504. package/data/skills/deep-visual-proteomics-agent/SKILL.md +149 -0
  505. package/data/skills/deepchem/SKILL.md +591 -0
  506. package/data/skills/deeptools/SKILL.md +525 -0
  507. package/data/skills/depmap/SKILL.md +300 -0
  508. package/data/skills/diffdock/SKILL.md +477 -0
  509. package/data/skills/differentiation-schemes/SKILL.md +159 -0
  510. package/data/skills/digital-twin-clinical-agent/SKILL.md +228 -0
  511. package/data/skills/dispatching-parallel-agents/SKILL.md +180 -0
  512. package/data/skills/dnanexus-integration/SKILL.md +376 -0
  513. package/data/skills/doc-coauthoring/SKILL.md +375 -0
  514. package/data/skills/docx/SKILL.md +590 -0
  515. package/data/skills/docx-official/SKILL.md +197 -0
  516. package/data/skills/drug-discovery-search/SKILL.md +214 -0
  517. package/data/skills/drug-interaction-checker/SKILL.md +56 -0
  518. package/data/skills/drug-labels-search/SKILL.md +211 -0
  519. package/data/skills/drug-photo/SKILL.md +149 -0
  520. package/data/skills/drugbank-database/SKILL.md +184 -0
  521. package/data/skills/drugbank-search/SKILL.md +211 -0
  522. package/data/skills/ehr-fhir-integration/SKILL.md +60 -0
  523. package/data/skills/emergency-card/SKILL.md +426 -0
  524. package/data/skills/ena-database/SKILL.md +198 -0
  525. package/data/skills/ensembl-database/SKILL.md +305 -0
  526. package/data/skills/epidemiologist-analyst/SKILL.md +1844 -0
  527. package/data/skills/epigenomics-methylgpt-agent/SKILL.md +111 -0
  528. package/data/skills/equity-scorer/SKILL.md +182 -0
  529. package/data/skills/esm/SKILL.md +300 -0
  530. package/data/skills/etetoolkit/SKILL.md +617 -0
  531. package/data/skills/executing-plans/SKILL.md +84 -0
  532. package/data/skills/exosome-ev-analysis-agent/SKILL.md +171 -0
  533. package/data/skills/exploratory-data-analysis/SKILL.md +440 -0
  534. package/data/skills/family-health-analyzer/SKILL.md +137 -0
  535. package/data/skills/fastq-analysis/SKILL.md +191 -0
  536. package/data/skills/fda-database/SKILL.md +512 -0
  537. package/data/skills/fhir-developer-skill/SKILL.md +294 -0
  538. package/data/skills/fhir-development/SKILL.md +35 -0
  539. package/data/skills/find-skills/SKILL.md +133 -0
  540. package/data/skills/finishing-a-development-branch/SKILL.md +200 -0
  541. package/data/skills/fitness-analyzer/SKILL.md +431 -0
  542. package/data/skills/flowio/SKILL.md +602 -0
  543. package/data/skills/foldseek/SKILL.md +179 -0
  544. package/data/skills/galaxy-bridge/SKILL.md +215 -0
  545. package/data/skills/gene-database/SKILL.md +173 -0
  546. package/data/skills/gene-panel-design-agent/SKILL.md +192 -0
  547. package/data/skills/geniml/SKILL.md +312 -0
  548. package/data/skills/genome-compare/SKILL.md +127 -0
  549. package/data/skills/geo-database/SKILL.md +809 -0
  550. package/data/skills/geopandas/SKILL.md +245 -0
  551. package/data/skills/gget/SKILL.md +865 -0
  552. package/data/skills/ginkgo-cloud-lab/SKILL.md +56 -0
  553. package/data/skills/glycoengineering/SKILL.md +338 -0
  554. package/data/skills/gnomad-database/SKILL.md +395 -0
  555. package/data/skills/goal-analyzer/SKILL.md +605 -0
  556. package/data/skills/grief-companion/SKILL.md +250 -0
  557. package/data/skills/gsea-enrichment/SKILL.md +151 -0
  558. package/data/skills/gtars/SKILL.md +279 -0
  559. package/data/skills/gtex-database/SKILL.md +315 -0
  560. package/data/skills/gwas-database/SKILL.md +602 -0
  561. package/data/skills/gwas-lookup/SKILL.md +122 -0
  562. package/data/skills/gwas-prs/SKILL.md +178 -0
  563. package/data/skills/health-trend-analyzer/SKILL.md +451 -0
  564. package/data/skills/hemoglobinopathy-analysis-agent/SKILL.md +167 -0
  565. package/data/skills/hipaa-compliance/SKILL.md +230 -0
  566. package/data/skills/histolab/SKILL.md +672 -0
  567. package/data/skills/hmdb-database/SKILL.md +190 -0
  568. package/data/skills/hrd-analysis-agent/SKILL.md +184 -0
  569. package/data/skills/hrv-alexithymia-expert/SKILL.md +151 -0
  570. package/data/skills/hypogenic/SKILL.md +649 -0
  571. package/data/skills/hypothesis-generation/SKILL.md +286 -0
  572. package/data/skills/imaging-data-commons/SKILL.md +843 -0
  573. package/data/skills/immune-checkpoint-combination-agent/SKILL.md +170 -0
  574. package/data/skills/infographics/SKILL.md +563 -0
  575. package/data/skills/instrument-data-to-allotrope/SKILL.md +280 -0
  576. package/data/skills/interpro-database/SKILL.md +305 -0
  577. package/data/skills/ipsae/SKILL.md +190 -0
  578. package/data/skills/iso-13485-certification/SKILL.md +678 -0
  579. package/data/skills/jaspar-database/SKILL.md +351 -0
  580. package/data/skills/jungian-psychologist/SKILL.md +191 -0
  581. package/data/skills/kegg-database/SKILL.md +371 -0
  582. package/data/skills/knowledge-synthesis/SKILL.md +283 -0
  583. package/data/skills/kragen-knowledge-graph/SKILL.md +68 -0
  584. package/data/skills/lab-results/SKILL.md +35 -0
  585. package/data/skills/labarchive-integration/SKILL.md +262 -0
  586. package/data/skills/labstep/SKILL.md +208 -0
  587. package/data/skills/lamindb/SKILL.md +384 -0
  588. package/data/skills/latchbio-integration/SKILL.md +347 -0
  589. package/data/skills/latex-posters/SKILL.md +1602 -0
  590. package/data/skills/leads-literature-mining/SKILL.md +68 -0
  591. package/data/skills/ligandmpnn/SKILL.md +170 -0
  592. package/data/skills/linear-solvers/SKILL.md +165 -0
  593. package/data/skills/liquid-biopsy-analytics-agent/SKILL.md +171 -0
  594. package/data/skills/lit-synthesizer/SKILL.md +53 -0
  595. package/data/skills/literature-review/SKILL.md +584 -0
  596. package/data/skills/literature-search/SKILL.md +214 -0
  597. package/data/skills/lobster-bioinformatics/SKILL.md +305 -0
  598. package/data/skills/long-read-sequencing-agent/SKILL.md +181 -0
  599. package/data/skills/mage-antibody-generator/SKILL.md +54 -0
  600. package/data/skills/markdown-mermaid-writing/SKILL.md +327 -0
  601. package/data/skills/markitdown/SKILL.md +486 -0
  602. package/data/skills/matchms/SKILL.md +197 -0
  603. package/data/skills/matplotlib/SKILL.md +359 -0
  604. package/data/skills/mcpmed-bioinformatics-server/SKILL.md +42 -0
  605. package/data/skills/medchem/SKILL.md +400 -0
  606. package/data/skills/medea-therapeutic-discovery/SKILL.md +45 -0
  607. package/data/skills/medical-entity-extractor/SKILL.md +144 -0
  608. package/data/skills/medical-imaging-review/SKILL.md +170 -0
  609. package/data/skills/medical-research-toolkit/SKILL.md +273 -0
  610. package/data/skills/medrxiv-search/SKILL.md +211 -0
  611. package/data/skills/mental-health-analyzer/SKILL.md +981 -0
  612. package/data/skills/mesh-generation/SKILL.md +149 -0
  613. package/data/skills/metabolomics-workbench-database/SKILL.md +253 -0
  614. package/data/skills/microbiome-cancer-agent/SKILL.md +180 -0
  615. package/data/skills/modern-drug-rehab-computer/SKILL.md +392 -0
  616. package/data/skills/molecular-dynamics/SKILL.md +457 -0
  617. package/data/skills/molecular-glue-discovery-agent/SKILL.md +224 -0
  618. package/data/skills/molecule-evolution-agent/SKILL.md +62 -0
  619. package/data/skills/molfeat/SKILL.md +505 -0
  620. package/data/skills/monarch-database/SKILL.md +372 -0
  621. package/data/skills/mpn-progression-monitor-agent/SKILL.md +228 -0
  622. package/data/skills/mpn-research-assistant/SKILL.md +197 -0
  623. package/data/skills/mrd-edge-detection-agent/SKILL.md +213 -0
  624. package/data/skills/multi-ancestry-prs-agent/SKILL.md +224 -0
  625. package/data/skills/multi-search-engine/SKILL.md +110 -0
  626. package/data/skills/multimodal-medical-imaging/SKILL.md +59 -0
  627. package/data/skills/multimodal-radpath-fusion-agent/SKILL.md +213 -0
  628. package/data/skills/myeloma-mrd-agent/SKILL.md +184 -0
  629. package/data/skills/networkx/SKILL.md +435 -0
  630. package/data/skills/neurokit2/SKILL.md +350 -0
  631. package/data/skills/neuropixels-analysis/SKILL.md +344 -0
  632. package/data/skills/nextflow-development/SKILL.md +290 -0
  633. package/data/skills/ngs-analysis/SKILL.md +183 -0
  634. package/data/skills/nicheformer-spatial-agent/SKILL.md +197 -0
  635. package/data/skills/nk-cell-therapy-agent/SKILL.md +186 -0
  636. package/data/skills/nonlinear-solvers/SKILL.md +180 -0
  637. package/data/skills/numerical-integration/SKILL.md +166 -0
  638. package/data/skills/numerical-stability/SKILL.md +149 -0
  639. package/data/skills/nutrition-analyzer/SKILL.md +775 -0
  640. package/data/skills/occupational-health-analyzer/SKILL.md +386 -0
  641. package/data/skills/omero-integration/SKILL.md +245 -0
  642. package/data/skills/ontology-explorer/SKILL.md +168 -0
  643. package/data/skills/ontology-mapper/SKILL.md +171 -0
  644. package/data/skills/ontology-validator/SKILL.md +136 -0
  645. package/data/skills/open-notebook/SKILL.md +289 -0
  646. package/data/skills/open-targets-search/SKILL.md +211 -0
  647. package/data/skills/openalex-database/SKILL.md +488 -0
  648. package/data/skills/opentargets-database/SKILL.md +367 -0
  649. package/data/skills/opentrons-integration/SKILL.md +567 -0
  650. package/data/skills/opentrons-protocol-agent/SKILL.md +58 -0
  651. package/data/skills/organoid-drug-response-agent/SKILL.md +189 -0
  652. package/data/skills/pan-cancer-multiomics-agent/SKILL.md +159 -0
  653. package/data/skills/paper-2-web/SKILL.md +495 -0
  654. package/data/skills/parameter-optimization/SKILL.md +141 -0
  655. package/data/skills/patents-search/SKILL.md +211 -0
  656. package/data/skills/pathml/SKILL.md +160 -0
  657. package/data/skills/patiently-ai/SKILL.md +103 -0
  658. package/data/skills/pdb/SKILL.md +217 -0
  659. package/data/skills/pdb-database/SKILL.md +303 -0
  660. package/data/skills/pdf/SKILL.md +314 -0
  661. package/data/skills/pdf-anthropic/SKILL.md +294 -0
  662. package/data/skills/pdf-processing/SKILL.md +149 -0
  663. package/data/skills/pdf-processing-pro/SKILL.md +296 -0
  664. package/data/skills/pdx-model-analysis-agent/SKILL.md +169 -0
  665. package/data/skills/peer-review/SKILL.md +565 -0
  666. package/data/skills/performance-profiling/SKILL.md +255 -0
  667. package/data/skills/perplexity-search/SKILL.md +441 -0
  668. package/data/skills/pharmacogenomics-agent/SKILL.md +143 -0
  669. package/data/skills/pharmgx-reporter/SKILL.md +134 -0
  670. package/data/skills/phylogenetics/SKILL.md +404 -0
  671. package/data/skills/plotly/SKILL.md +265 -0
  672. package/data/skills/polars/SKILL.md +385 -0
  673. package/data/skills/popeve-variant-predictor-agent/SKILL.md +213 -0
  674. package/data/skills/post-processing/SKILL.md +338 -0
  675. package/data/skills/pptx/SKILL.md +232 -0
  676. package/data/skills/pptx-official/SKILL.md +484 -0
  677. package/data/skills/pptx-posters/SKILL.md +414 -0
  678. package/data/skills/precision-oncology-agent/SKILL.md +53 -0
  679. package/data/skills/prior-auth-coworker/SKILL.md +60 -0
  680. package/data/skills/prior-auth-review-skill/SKILL.md +360 -0
  681. package/data/skills/profile-report/SKILL.md +120 -0
  682. package/data/skills/protac-design-agent/SKILL.md +220 -0
  683. package/data/skills/protein-design-workflow/SKILL.md +199 -0
  684. package/data/skills/protein-qc/SKILL.md +300 -0
  685. package/data/skills/protein-structure-prediction/SKILL.md +59 -0
  686. package/data/skills/proteinmpnn/SKILL.md +279 -0
  687. package/data/skills/protocolsio-integration/SKILL.md +415 -0
  688. package/data/skills/prs-net-deep-learning-agent/SKILL.md +232 -0
  689. package/data/skills/psychologist-analyst/SKILL.md +1888 -0
  690. package/data/skills/pubchem-database/SKILL.md +568 -0
  691. package/data/skills/pubmed-database/SKILL.md +454 -0
  692. package/data/skills/pubmed-search/SKILL.md +103 -0
  693. package/data/skills/pydeseq2/SKILL.md +553 -0
  694. package/data/skills/pydicom/SKILL.md +428 -0
  695. package/data/skills/pyhealth/SKILL.md +485 -0
  696. package/data/skills/pylabrobot/SKILL.md +179 -0
  697. package/data/skills/pymc/SKILL.md +566 -0
  698. package/data/skills/pymoo/SKILL.md +565 -0
  699. package/data/skills/pyopenms/SKILL.md +211 -0
  700. package/data/skills/pysam/SKILL.md +259 -0
  701. package/data/skills/pytdc/SKILL.md +454 -0
  702. package/data/skills/pytorch-lightning/SKILL.md +172 -0
  703. package/data/skills/pyzotero/SKILL.md +111 -0
  704. package/data/skills/radgpt-radiology-reporter/SKILL.md +67 -0
  705. package/data/skills/radiomics-pathomics-fusion-agent/SKILL.md +221 -0
  706. package/data/skills/rdkit/SKILL.md +763 -0
  707. package/data/skills/reactome-database/SKILL.md +272 -0
  708. package/data/skills/receiving-code-review/SKILL.md +213 -0
  709. package/data/skills/recovery-community-moderator/SKILL.md +175 -0
  710. package/data/skills/regulatory-drafter/SKILL.md +56 -0
  711. package/data/skills/regulatory-drafting/SKILL.md +35 -0
  712. package/data/skills/rehabilitation-analyzer/SKILL.md +636 -0
  713. package/data/skills/repro-enforcer/SKILL.md +50 -0
  714. package/data/skills/requesting-code-review/SKILL.md +105 -0
  715. package/data/skills/research-grants/SKILL.md +935 -0
  716. package/data/skills/research-literature/SKILL.md +35 -0
  717. package/data/skills/research-lookup/SKILL.md +502 -0
  718. package/data/skills/rfdiffusion/SKILL.md +306 -0
  719. package/data/skills/rna-velocity-agent/SKILL.md +174 -0
  720. package/data/skills/scanpy/SKILL.md +380 -0
  721. package/data/skills/scfoundation-model-agent/SKILL.md +210 -0
  722. package/data/skills/scientific-brainstorming/SKILL.md +185 -0
  723. package/data/skills/scientific-critical-thinking/SKILL.md +566 -0
  724. package/data/skills/scientific-manuscript/SKILL.md +181 -0
  725. package/data/skills/scientific-problem-selection/SKILL.md +269 -0
  726. package/data/skills/scientific-schematics/SKILL.md +619 -0
  727. package/data/skills/scientific-slides/SKILL.md +1154 -0
  728. package/data/skills/scientific-visualization/SKILL.md +773 -0
  729. package/data/skills/scientific-writing/SKILL.md +483 -0
  730. package/data/skills/scikit-bio/SKILL.md +431 -0
  731. package/data/skills/scikit-learn/SKILL.md +515 -0
  732. package/data/skills/scikit-survival/SKILL.md +393 -0
  733. package/data/skills/scrna-orchestrator/SKILL.md +204 -0
  734. package/data/skills/scrna-qc/SKILL.md +43 -0
  735. package/data/skills/scvelo/SKILL.md +321 -0
  736. package/data/skills/scvi-tools/SKILL.md +184 -0
  737. package/data/skills/seaborn/SKILL.md +671 -0
  738. package/data/skills/search-strategy/SKILL.md +247 -0
  739. package/data/skills/seq-wrangler/SKILL.md +58 -0
  740. package/data/skills/shap/SKILL.md +560 -0
  741. package/data/skills/simo-multiomics-integration-agent/SKILL.md +178 -0
  742. package/data/skills/simpy/SKILL.md +423 -0
  743. package/data/skills/simulation-orchestrator/SKILL.md +230 -0
  744. package/data/skills/simulation-validator/SKILL.md +195 -0
  745. package/data/skills/single-annotation/SKILL.md +129 -0
  746. package/data/skills/single-cell-rna-qc/SKILL.md +175 -0
  747. package/data/skills/single-cellphone-db/SKILL.md +68 -0
  748. package/data/skills/single-clustering/SKILL.md +75 -0
  749. package/data/skills/single-downstream-analysis/SKILL.md +150 -0
  750. package/data/skills/single-multiomics/SKILL.md +44 -0
  751. package/data/skills/single-preprocessing/SKILL.md +184 -0
  752. package/data/skills/single-to-spatial-mapping/SKILL.md +48 -0
  753. package/data/skills/single-trajectory/SKILL.md +62 -0
  754. package/data/skills/sleep-analyzer/SKILL.md +773 -0
  755. package/data/skills/slurm-job-script-generator/SKILL.md +135 -0
  756. package/data/skills/solublempnn/SKILL.md +165 -0
  757. package/data/skills/spatial-agent/SKILL.md +56 -0
  758. package/data/skills/spatial-epigenomics-agent/SKILL.md +163 -0
  759. package/data/skills/spatial-transcriptomics-agent/SKILL.md +75 -0
  760. package/data/skills/spatial-transcriptomics-analysis/SKILL.md +72 -0
  761. package/data/skills/spatial-transcriptomics-analysis/STAgent/SKILL.md +75 -0
  762. package/data/skills/spatial-transcriptomics-analysis/SpatialAgent/SKILL.md +56 -0
  763. package/data/skills/spatial-transcriptomics-analysis/bioSkills/image-analysis/SKILL.md +266 -0
  764. package/data/skills/spatial-transcriptomics-analysis/bioSkills/spatial-communication/SKILL.md +287 -0
  765. package/data/skills/spatial-transcriptomics-analysis/bioSkills/spatial-data-io/SKILL.md +243 -0
  766. package/data/skills/spatial-transcriptomics-analysis/bioSkills/spatial-deconvolution/SKILL.md +298 -0
  767. package/data/skills/spatial-transcriptomics-analysis/bioSkills/spatial-domains/SKILL.md +229 -0
  768. package/data/skills/spatial-transcriptomics-analysis/bioSkills/spatial-multiomics/SKILL.md +172 -0
  769. package/data/skills/spatial-transcriptomics-analysis/bioSkills/spatial-neighbors/SKILL.md +189 -0
  770. package/data/skills/spatial-transcriptomics-analysis/bioSkills/spatial-preprocessing/SKILL.md +232 -0
  771. package/data/skills/spatial-transcriptomics-analysis/bioSkills/spatial-proteomics/SKILL.md +127 -0
  772. package/data/skills/spatial-transcriptomics-analysis/bioSkills/spatial-statistics/SKILL.md +225 -0
  773. package/data/skills/spatial-transcriptomics-analysis/bioSkills/spatial-visualization/SKILL.md +270 -0
  774. package/data/skills/spatial-tutorials/SKILL.md +87 -0
  775. package/data/skills/speech-pathology-ai/SKILL.md +184 -0
  776. package/data/skills/statistical-analysis/SKILL.md +626 -0
  777. package/data/skills/statsmodels/SKILL.md +608 -0
  778. package/data/skills/string-database/SKILL.md +528 -0
  779. package/data/skills/struct-predictor/SKILL.md +52 -0
  780. package/data/skills/subagent-driven-development/SKILL.md +242 -0
  781. package/data/skills/systematic-debugging/SKILL.md +296 -0
  782. package/data/skills/tcell-exhaustion-analysis-agent/SKILL.md +139 -0
  783. package/data/skills/tcga-preprocessing/SKILL.md +49 -0
  784. package/data/skills/tcm-constitution-analyzer/SKILL.md +664 -0
  785. package/data/skills/tcr-pmhc-prediction-agent/SKILL.md +226 -0
  786. package/data/skills/tcr-repertoire-analysis-agent/SKILL.md +218 -0
  787. package/data/skills/test-driven-development/SKILL.md +371 -0
  788. package/data/skills/tiledbvcf/SKILL.md +459 -0
  789. package/data/skills/time-resolved-cryoem-agent/SKILL.md +223 -0
  790. package/data/skills/time-stepping/SKILL.md +140 -0
  791. package/data/skills/timesfm-forecasting/SKILL.md +785 -0
  792. package/data/skills/tme-immune-profiling-agent/SKILL.md +220 -0
  793. package/data/skills/tooluniverse-adverse-event-detection/SKILL.md +1115 -0
  794. package/data/skills/tooluniverse-antibody-engineering/SKILL.md +1581 -0
  795. package/data/skills/tooluniverse-binder-discovery/SKILL.md +1459 -0
  796. package/data/skills/tooluniverse-cancer-variant-interpretation/SKILL.md +971 -0
  797. package/data/skills/tooluniverse-chemical-compound-retrieval/SKILL.md +322 -0
  798. package/data/skills/tooluniverse-chemical-safety/SKILL.md +733 -0
  799. package/data/skills/tooluniverse-clinical-guidelines/SKILL.md +399 -0
  800. package/data/skills/tooluniverse-clinical-trial-design/SKILL.md +1195 -0
  801. package/data/skills/tooluniverse-clinical-trial-matching/SKILL.md +1333 -0
  802. package/data/skills/tooluniverse-crispr-screen-analysis/SKILL.md +900 -0
  803. package/data/skills/tooluniverse-disease-research/SKILL.md +630 -0
  804. package/data/skills/tooluniverse-drug-drug-interaction/SKILL.md +73 -0
  805. package/data/skills/tooluniverse-drug-repurposing/SKILL.md +595 -0
  806. package/data/skills/tooluniverse-drug-research/SKILL.md +1642 -0
  807. package/data/skills/tooluniverse-drug-target-validation/SKILL.md +1206 -0
  808. package/data/skills/tooluniverse-epigenomics/SKILL.md +1489 -0
  809. package/data/skills/tooluniverse-expression-data-retrieval/SKILL.md +389 -0
  810. package/data/skills/tooluniverse-gene-enrichment/SKILL.md +402 -0
  811. package/data/skills/tooluniverse-gwas-drug-discovery/SKILL.md +576 -0
  812. package/data/skills/tooluniverse-gwas-finemapping/SKILL.md +309 -0
  813. package/data/skills/tooluniverse-gwas-snp-interpretation/SKILL.md +223 -0
  814. package/data/skills/tooluniverse-gwas-study-explorer/SKILL.md +342 -0
  815. package/data/skills/tooluniverse-gwas-trait-to-gene/SKILL.md +236 -0
  816. package/data/skills/tooluniverse-image-analysis/SKILL.md +439 -0
  817. package/data/skills/tooluniverse-immune-repertoire-analysis/SKILL.md +949 -0
  818. package/data/skills/tooluniverse-immunotherapy-response-prediction/SKILL.md +865 -0
  819. package/data/skills/tooluniverse-infectious-disease/SKILL.md +749 -0
  820. package/data/skills/tooluniverse-literature-deep-research/SKILL.md +1050 -0
  821. package/data/skills/tooluniverse-metabolomics/SKILL.md +298 -0
  822. package/data/skills/tooluniverse-metabolomics-analysis/SKILL.md +764 -0
  823. package/data/skills/tooluniverse-multi-omics-integration/SKILL.md +703 -0
  824. package/data/skills/tooluniverse-multiomic-disease-characterization/SKILL.md +1138 -0
  825. package/data/skills/tooluniverse-network-pharmacology/SKILL.md +1312 -0
  826. package/data/skills/tooluniverse-pharmacovigilance/SKILL.md +807 -0
  827. package/data/skills/tooluniverse-phylogenetics/SKILL.md +461 -0
  828. package/data/skills/tooluniverse-polygenic-risk-score/SKILL.md +397 -0
  829. package/data/skills/tooluniverse-precision-medicine-stratification/SKILL.md +1143 -0
  830. package/data/skills/tooluniverse-precision-oncology/SKILL.md +1091 -0
  831. package/data/skills/tooluniverse-protein-interactions/SKILL.md +446 -0
  832. package/data/skills/tooluniverse-protein-structure-retrieval/SKILL.md +416 -0
  833. package/data/skills/tooluniverse-protein-therapeutic-design/SKILL.md +637 -0
  834. package/data/skills/tooluniverse-proteomics-analysis/SKILL.md +843 -0
  835. package/data/skills/tooluniverse-rare-disease-diagnosis/SKILL.md +1257 -0
  836. package/data/skills/tooluniverse-rnaseq-deseq2/SKILL.md +536 -0
  837. package/data/skills/tooluniverse-sequence-retrieval/SKILL.md +419 -0
  838. package/data/skills/tooluniverse-single-cell/SKILL.md +719 -0
  839. package/data/skills/tooluniverse-spatial-omics-analysis/SKILL.md +1102 -0
  840. package/data/skills/tooluniverse-spatial-transcriptomics/SKILL.md +788 -0
  841. package/data/skills/tooluniverse-statistical-modeling/SKILL.md +557 -0
  842. package/data/skills/tooluniverse-structural-variant-analysis/SKILL.md +1356 -0
  843. package/data/skills/tooluniverse-systems-biology/SKILL.md +374 -0
  844. package/data/skills/tooluniverse-target-research/SKILL.md +1510 -0
  845. package/data/skills/tooluniverse-variant-analysis/SKILL.md +448 -0
  846. package/data/skills/tooluniverse-variant-interpretation/SKILL.md +1118 -0
  847. package/data/skills/torch-geometric/SKILL.md +674 -0
  848. package/data/skills/torch_geometric/SKILL.md +670 -0
  849. package/data/skills/torchdrug/SKILL.md +444 -0
  850. package/data/skills/tpd-ternary-complex-agent/SKILL.md +226 -0
  851. package/data/skills/transformers/SKILL.md +157 -0
  852. package/data/skills/travel-health-analyzer/SKILL.md +421 -0
  853. package/data/skills/treatment-plans/SKILL.md +1576 -0
  854. package/data/skills/trial-eligibility-agent/SKILL.md +54 -0
  855. package/data/skills/trialgpt-matching/SKILL.md +66 -0
  856. package/data/skills/tumor-clonal-evolution-agent/SKILL.md +134 -0
  857. package/data/skills/tumor-heterogeneity-agent/SKILL.md +216 -0
  858. package/data/skills/tumor-mutational-burden-agent/SKILL.md +188 -0
  859. package/data/skills/ukb-navigator/SKILL.md +113 -0
  860. package/data/skills/umap-learn/SKILL.md +473 -0
  861. package/data/skills/uniprot-database/SKILL.md +189 -0
  862. package/data/skills/universal-single-cell-annotator/SKILL.md +72 -0
  863. package/data/skills/using-git-worktrees/SKILL.md +218 -0
  864. package/data/skills/using-superpowers/SKILL.md +95 -0
  865. package/data/skills/usmle/SKILL.md +62 -0
  866. package/data/skills/uspto-database/SKILL.md +597 -0
  867. package/data/skills/vaex/SKILL.md +180 -0
  868. package/data/skills/varcadd-pathogenicity/SKILL.md +68 -0
  869. package/data/skills/variant-interpretation-acmg/SKILL.md +58 -0
  870. package/data/skills/variant-interpretation-acmg/bioSkills/clinical-interpretation/SKILL.md +334 -0
  871. package/data/skills/variant-interpretation-acmg/bioSkills/consensus-sequences/SKILL.md +343 -0
  872. package/data/skills/variant-interpretation-acmg/bioSkills/deepvariant/SKILL.md +279 -0
  873. package/data/skills/variant-interpretation-acmg/bioSkills/filtering-best-practices/SKILL.md +362 -0
  874. package/data/skills/variant-interpretation-acmg/bioSkills/gatk-variant-calling/SKILL.md +398 -0
  875. package/data/skills/variant-interpretation-acmg/bioSkills/joint-calling/SKILL.md +343 -0
  876. package/data/skills/variant-interpretation-acmg/bioSkills/structural-variant-calling/SKILL.md +256 -0
  877. package/data/skills/variant-interpretation-acmg/bioSkills/variant-annotation/SKILL.md +387 -0
  878. package/data/skills/variant-interpretation-acmg/bioSkills/variant-calling/SKILL.md +258 -0
  879. package/data/skills/variant-interpretation-acmg/bioSkills/variant-normalization/SKILL.md +304 -0
  880. package/data/skills/variant-interpretation-acmg/bioSkills/vcf-basics/SKILL.md +329 -0
  881. package/data/skills/variant-interpretation-acmg/bioSkills/vcf-manipulation/SKILL.md +398 -0
  882. package/data/skills/variant-interpretation-acmg/bioSkills/vcf-statistics/SKILL.md +424 -0
  883. package/data/skills/variant-interpretation-acmg/varCADD/SKILL.md +68 -0
  884. package/data/skills/vcf-annotator/SKILL.md +55 -0
  885. package/data/skills/verification-before-completion/SKILL.md +139 -0
  886. package/data/skills/virtual-lab-agent/SKILL.md +240 -0
  887. package/data/skills/wearable-analysis-agent/SKILL.md +70 -0
  888. package/data/skills/weightloss-analyzer/SKILL.md +320 -0
  889. package/data/skills/wellally-tech/SKILL.md +685 -0
  890. package/data/skills/wikipedia-search/SKILL.md +481 -0
  891. package/data/skills/writing-plans/SKILL.md +116 -0
  892. package/data/skills/writing-skills/SKILL.md +655 -0
  893. package/data/skills/xlsx/SKILL.md +292 -0
  894. package/data/skills/xlsx-official/SKILL.md +289 -0
  895. package/data/skills/zarr-python/SKILL.md +777 -0
  896. package/data/skills/zinc-database/SKILL.md +398 -0
  897. package/data/tools/__init__.py +8 -0
  898. package/data/tools/hpc.py +71 -0
  899. package/data/tools/hpc_client/__init__.py +8 -0
  900. package/data/tools/hpc_client/builders/__init__.py +12 -0
  901. package/data/tools/hpc_client/builders/alphafold.py +36 -0
  902. package/data/tools/hpc_client/builders/boltz.py +33 -0
  903. package/data/tools/hpc_client/builders/chai.py +30 -0
  904. package/data/tools/hpc_client/builders/immunebuilder.py +31 -0
  905. package/data/tools/hpc_client/builders/rfantibody.py +58 -0
  906. package/data/tools/hpc_client/builders/thermompnn.py +16 -0
  907. package/data/tools/hpc_client/hpc_api.py +41 -0
  908. package/data/tools/hpc_client/hpc_tools.py +218 -0
  909. package/data/tools/hpc_dynamic.py +71 -0
  910. package/data/tools/integrations/__init__.py +14 -0
  911. package/data/tools/integrations/adaptyv.py +107 -0
  912. package/data/tools/integrations/addgene.py +52 -0
  913. package/data/tools/integrations/api_internal.py +33 -0
  914. package/data/tools/molecular_biology.py +688 -0
  915. package/data/tools/pharmacology.py +67 -0
  916. package/data/workflows/bulk-omics-clustering/SKILL.md +501 -0
  917. package/data/workflows/bulk-omics-clustering/references/best_practices.md +395 -0
  918. package/data/workflows/bulk-omics-clustering/references/clustering_methods_comparison.md +288 -0
  919. package/data/workflows/bulk-omics-clustering/references/common-patterns.md +1136 -0
  920. package/data/workflows/bulk-omics-clustering/references/decision-guide.md +819 -0
  921. package/data/workflows/bulk-omics-clustering/references/distance_metrics_guide.md +388 -0
  922. package/data/workflows/bulk-omics-clustering/references/parameter_guide.md +396 -0
  923. package/data/workflows/bulk-omics-clustering/references/r-quick-start.md +105 -0
  924. package/data/workflows/bulk-omics-clustering/references/validation_metrics_guide.md +315 -0
  925. package/data/workflows/bulk-omics-clustering/scripts/characterize_clusters.py +255 -0
  926. package/data/workflows/bulk-omics-clustering/scripts/cluster_validation.py +449 -0
  927. package/data/workflows/bulk-omics-clustering/scripts/density_clustering.py +321 -0
  928. package/data/workflows/bulk-omics-clustering/scripts/dimensionality_reduction.py +328 -0
  929. package/data/workflows/bulk-omics-clustering/scripts/distance_metrics.py +251 -0
  930. package/data/workflows/bulk-omics-clustering/scripts/export_results.py +456 -0
  931. package/data/workflows/bulk-omics-clustering/scripts/hierarchical_clustering.R +229 -0
  932. package/data/workflows/bulk-omics-clustering/scripts/hierarchical_clustering.py +269 -0
  933. package/data/workflows/bulk-omics-clustering/scripts/kmeans_clustering.py +346 -0
  934. package/data/workflows/bulk-omics-clustering/scripts/load_example_data.R +171 -0
  935. package/data/workflows/bulk-omics-clustering/scripts/load_example_data.py +171 -0
  936. package/data/workflows/bulk-omics-clustering/scripts/model_based_clustering.py +370 -0
  937. package/data/workflows/bulk-omics-clustering/scripts/optimal_clusters.py +381 -0
  938. package/data/workflows/bulk-omics-clustering/scripts/plot_cluster_heatmap.R +141 -0
  939. package/data/workflows/bulk-omics-clustering/scripts/plot_clustering_results.py +452 -0
  940. package/data/workflows/bulk-omics-clustering/scripts/prepare_data.py +250 -0
  941. package/data/workflows/bulk-omics-clustering/scripts/stability_analysis.py +434 -0
  942. package/data/workflows/bulk-rnaseq-counts-to-de-deseq2/SKILL.md +505 -0
  943. package/data/workflows/bulk-rnaseq-counts-to-de-deseq2/references/comprehensive-reference.md +440 -0
  944. package/data/workflows/bulk-rnaseq-counts-to-de-deseq2/references/decision-guide.md +327 -0
  945. package/data/workflows/bulk-rnaseq-counts-to-de-deseq2/references/troubleshooting.md +456 -0
  946. package/data/workflows/bulk-rnaseq-counts-to-de-deseq2/references/usage-guide.md +75 -0
  947. package/data/workflows/bulk-rnaseq-counts-to-de-deseq2/scripts/basic_workflow.R +149 -0
  948. package/data/workflows/bulk-rnaseq-counts-to-de-deseq2/scripts/batch_correction.R +44 -0
  949. package/data/workflows/bulk-rnaseq-counts-to-de-deseq2/scripts/export_results.R +190 -0
  950. package/data/workflows/bulk-rnaseq-counts-to-de-deseq2/scripts/extract_results.R +242 -0
  951. package/data/workflows/bulk-rnaseq-counts-to-de-deseq2/scripts/load_example_data.R +250 -0
  952. package/data/workflows/bulk-rnaseq-counts-to-de-deseq2/scripts/multi_condition.R +50 -0
  953. package/data/workflows/bulk-rnaseq-counts-to-de-deseq2/scripts/qc_plots.R +410 -0
  954. package/data/workflows/bulk-rnaseq-counts-to-de-deseq2/scripts/transformations.R +218 -0
  955. package/data/workflows/chip-atlas-diff-analysis/SKILL.md +222 -0
  956. package/data/workflows/chip-atlas-diff-analysis/references/chipatlas_diff_api_format.md +106 -0
  957. package/data/workflows/chip-atlas-diff-analysis/references/diff_analysis_methods.md +89 -0
  958. package/data/workflows/chip-atlas-diff-analysis/references/output_format.md +78 -0
  959. package/data/workflows/chip-atlas-diff-analysis/scripts/__init__.py +1 -0
  960. package/data/workflows/chip-atlas-diff-analysis/scripts/annotate_genes.py +144 -0
  961. package/data/workflows/chip-atlas-diff-analysis/scripts/export_all.py +498 -0
  962. package/data/workflows/chip-atlas-diff-analysis/scripts/filter_regions.py +176 -0
  963. package/data/workflows/chip-atlas-diff-analysis/scripts/generate_all_plots.py +321 -0
  964. package/data/workflows/chip-atlas-diff-analysis/scripts/load_example_data.py +149 -0
  965. package/data/workflows/chip-atlas-diff-analysis/scripts/load_user_data.py +211 -0
  966. package/data/workflows/chip-atlas-diff-analysis/scripts/parse_bed_results.py +240 -0
  967. package/data/workflows/chip-atlas-diff-analysis/scripts/qc_checks.py +621 -0
  968. package/data/workflows/chip-atlas-diff-analysis/scripts/query_chipatlas_api.py +329 -0
  969. package/data/workflows/chip-atlas-diff-analysis/scripts/run_diff_workflow.py +256 -0
  970. package/data/workflows/chip-atlas-peak-enrichment/SKILL.md +212 -0
  971. package/data/workflows/chip-atlas-peak-enrichment/references/chipatlas_metadata_format.md +115 -0
  972. package/data/workflows/chip-atlas-peak-enrichment/references/enrichment_statistics.md +145 -0
  973. package/data/workflows/chip-atlas-peak-enrichment/references/peak_thresholds.md +63 -0
  974. package/data/workflows/chip-atlas-peak-enrichment/references/promoter_definitions.md +69 -0
  975. package/data/workflows/chip-atlas-peak-enrichment/scripts/__init__.py +1 -0
  976. package/data/workflows/chip-atlas-peak-enrichment/scripts/convert_genes_to_regions.py +271 -0
  977. package/data/workflows/chip-atlas-peak-enrichment/scripts/export_all.py +456 -0
  978. package/data/workflows/chip-atlas-peak-enrichment/scripts/filter_experiments.py +116 -0
  979. package/data/workflows/chip-atlas-peak-enrichment/scripts/generate_all_plots.py +280 -0
  980. package/data/workflows/chip-atlas-peak-enrichment/scripts/load_example_data.py +96 -0
  981. package/data/workflows/chip-atlas-peak-enrichment/scripts/load_user_data.py +183 -0
  982. package/data/workflows/chip-atlas-peak-enrichment/scripts/query_chipatlas_api.py +349 -0
  983. package/data/workflows/chip-atlas-peak-enrichment/scripts/run_enrichment_workflow.py +271 -0
  984. package/data/workflows/chip-atlas-target-genes/SKILL.md +230 -0
  985. package/data/workflows/chip-atlas-target-genes/references/macs2_binding_scores.md +89 -0
  986. package/data/workflows/chip-atlas-target-genes/references/string_scores.md +58 -0
  987. package/data/workflows/chip-atlas-target-genes/references/target_genes_data_format.md +73 -0
  988. package/data/workflows/chip-atlas-target-genes/scripts/__init__.py +0 -0
  989. package/data/workflows/chip-atlas-target-genes/scripts/download_target_genes.py +200 -0
  990. package/data/workflows/chip-atlas-target-genes/scripts/export_all.py +340 -0
  991. package/data/workflows/chip-atlas-target-genes/scripts/filter_targets.py +205 -0
  992. package/data/workflows/chip-atlas-target-genes/scripts/generate_all_plots.py +330 -0
  993. package/data/workflows/chip-atlas-target-genes/scripts/load_example_query.py +61 -0
  994. package/data/workflows/chip-atlas-target-genes/scripts/load_user_query.py +47 -0
  995. package/data/workflows/chip-atlas-target-genes/scripts/run_target_genes_workflow.py +141 -0
  996. package/data/workflows/clinicaltrials-landscape/SKILL.md +257 -0
  997. package/data/workflows/clinicaltrials-landscape/references/api-parameters.md +181 -0
  998. package/data/workflows/clinicaltrials-landscape/references/mechanisms.md +141 -0
  999. package/data/workflows/clinicaltrials-landscape/references/output-schema.md +184 -0
  1000. package/data/workflows/clinicaltrials-landscape/scripts/__init__.py +1 -0
  1001. package/data/workflows/clinicaltrials-landscape/scripts/classify_mechanisms.py +359 -0
  1002. package/data/workflows/clinicaltrials-landscape/scripts/compile_trials.py +579 -0
  1003. package/data/workflows/clinicaltrials-landscape/scripts/disease_config.py +161 -0
  1004. package/data/workflows/clinicaltrials-landscape/scripts/export_all.py +242 -0
  1005. package/data/workflows/clinicaltrials-landscape/scripts/generate_landscape_plots.py +761 -0
  1006. package/data/workflows/clinicaltrials-landscape/scripts/generate_pdf_report.py +1465 -0
  1007. package/data/workflows/clinicaltrials-landscape/scripts/generate_report.py +1813 -0
  1008. package/data/workflows/clinicaltrials-landscape/scripts/query_clinicaltrials.py +307 -0
  1009. package/data/workflows/coexpression-network/SKILL.md +344 -0
  1010. package/data/workflows/coexpression-network/references/parameter-tuning-guide.md +591 -0
  1011. package/data/workflows/coexpression-network/references/troubleshooting.md +483 -0
  1012. package/data/workflows/coexpression-network/references/wgcna-best-practices.md +563 -0
  1013. package/data/workflows/coexpression-network/references/wgcna-reference.md +538 -0
  1014. package/data/workflows/coexpression-network/scripts/build_network.R +43 -0
  1015. package/data/workflows/coexpression-network/scripts/correlate_modules_traits.R +92 -0
  1016. package/data/workflows/coexpression-network/scripts/export_wgcna_results.R +117 -0
  1017. package/data/workflows/coexpression-network/scripts/identify_hub_genes.R +63 -0
  1018. package/data/workflows/coexpression-network/scripts/load_example_data.R +214 -0
  1019. package/data/workflows/coexpression-network/scripts/module_enrichment.R +159 -0
  1020. package/data/workflows/coexpression-network/scripts/pick_soft_power.R +70 -0
  1021. package/data/workflows/coexpression-network/scripts/plot_all_wgcna.R +104 -0
  1022. package/data/workflows/coexpression-network/scripts/plot_eigengene_heatmap.R +65 -0
  1023. package/data/workflows/coexpression-network/scripts/plot_hub_genes.R +70 -0
  1024. package/data/workflows/coexpression-network/scripts/plot_module_dendrogram.R +50 -0
  1025. package/data/workflows/coexpression-network/scripts/plotting_helpers.R +87 -0
  1026. package/data/workflows/coexpression-network/scripts/prepare_wgcna_data.R +73 -0
  1027. package/data/workflows/coexpression-network/scripts/wgcna_workflow.R +93 -0
  1028. package/data/workflows/experimental-design-statistics/SKILL.md +408 -0
  1029. package/data/workflows/experimental-design-statistics/references/batch_effect_mitigation.md +756 -0
  1030. package/data/workflows/experimental-design-statistics/references/cv_tissue_database.csv +30 -0
  1031. package/data/workflows/experimental-design-statistics/references/experimental_design_best_practices.md +515 -0
  1032. package/data/workflows/experimental-design-statistics/references/multiple_testing_guide.md +730 -0
  1033. package/data/workflows/experimental-design-statistics/references/power_analysis_guidelines.md +635 -0
  1034. package/data/workflows/experimental-design-statistics/references/qc_guidelines.md +310 -0
  1035. package/data/workflows/experimental-design-statistics/references/software_requirements.md +328 -0
  1036. package/data/workflows/experimental-design-statistics/references/troubleshooting_guide.md +510 -0
  1037. package/data/workflows/experimental-design-statistics/scripts/batch_assignment.R +302 -0
  1038. package/data/workflows/experimental-design-statistics/scripts/batch_validation.R +342 -0
  1039. package/data/workflows/experimental-design-statistics/scripts/export_design.R +352 -0
  1040. package/data/workflows/experimental-design-statistics/scripts/load_example_data.R +204 -0
  1041. package/data/workflows/experimental-design-statistics/scripts/multiple_testing.R +417 -0
  1042. package/data/workflows/experimental-design-statistics/scripts/plot_power_curves.R +317 -0
  1043. package/data/workflows/experimental-design-statistics/scripts/power_atacseq.R +229 -0
  1044. package/data/workflows/experimental-design-statistics/scripts/power_pilot_based.R +289 -0
  1045. package/data/workflows/experimental-design-statistics/scripts/power_rnaseq.R +247 -0
  1046. package/data/workflows/experimental-design-statistics/scripts/sample_size_de.R +327 -0
  1047. package/data/workflows/experimental-design-statistics/scripts/sample_size_scrna.R +304 -0
  1048. package/data/workflows/functional-enrichment-from-degs/SKILL.md +387 -0
  1049. package/data/workflows/functional-enrichment-from-degs/references/database_guide.md +354 -0
  1050. package/data/workflows/functional-enrichment-from-degs/references/decision-guide.md +546 -0
  1051. package/data/workflows/functional-enrichment-from-degs/references/gsea_ora_comparison.md +213 -0
  1052. package/data/workflows/functional-enrichment-from-degs/references/gsea_ora_validation_framework.md +483 -0
  1053. package/data/workflows/functional-enrichment-from-degs/references/interpretation_guidelines.md +374 -0
  1054. package/data/workflows/functional-enrichment-from-degs/references/method-reference.md +742 -0
  1055. package/data/workflows/functional-enrichment-from-degs/scripts/export_results.R +190 -0
  1056. package/data/workflows/functional-enrichment-from-degs/scripts/generate_plots.R +240 -0
  1057. package/data/workflows/functional-enrichment-from-degs/scripts/get_msigdb_genesets.R +75 -0
  1058. package/data/workflows/functional-enrichment-from-degs/scripts/load_de_results.R +60 -0
  1059. package/data/workflows/functional-enrichment-from-degs/scripts/load_example_data.R +212 -0
  1060. package/data/workflows/functional-enrichment-from-degs/scripts/prepare_gene_lists.R +92 -0
  1061. package/data/workflows/functional-enrichment-from-degs/scripts/run_gsea.R +44 -0
  1062. package/data/workflows/functional-enrichment-from-degs/scripts/run_ora.R +53 -0
  1063. package/data/workflows/genetic-variant-annotation/SKILL.md +440 -0
  1064. package/data/workflows/genetic-variant-annotation/references/auto_installation_implementation.md +274 -0
  1065. package/data/workflows/genetic-variant-annotation/references/consequence_terms.md +392 -0
  1066. package/data/workflows/genetic-variant-annotation/references/filtering_strategies.md +808 -0
  1067. package/data/workflows/genetic-variant-annotation/references/installation_guide.md +557 -0
  1068. package/data/workflows/genetic-variant-annotation/references/pathogenicity_interpretation.md +473 -0
  1069. package/data/workflows/genetic-variant-annotation/references/qc_guidelines.md +524 -0
  1070. package/data/workflows/genetic-variant-annotation/references/snpeff_best_practices.md +481 -0
  1071. package/data/workflows/genetic-variant-annotation/references/tool_selection_guide.md +433 -0
  1072. package/data/workflows/genetic-variant-annotation/references/troubleshooting_guide.md +678 -0
  1073. package/data/workflows/genetic-variant-annotation/references/vep_best_practices.md +450 -0
  1074. package/data/workflows/genetic-variant-annotation/scripts/annotate_genes.py +243 -0
  1075. package/data/workflows/genetic-variant-annotation/scripts/export_results.py +450 -0
  1076. package/data/workflows/genetic-variant-annotation/scripts/filter_variants.py +365 -0
  1077. package/data/workflows/genetic-variant-annotation/scripts/install_tools.py +246 -0
  1078. package/data/workflows/genetic-variant-annotation/scripts/load_example_data.py +166 -0
  1079. package/data/workflows/genetic-variant-annotation/scripts/parse_snpeff_output.py +283 -0
  1080. package/data/workflows/genetic-variant-annotation/scripts/parse_vep_output.py +257 -0
  1081. package/data/workflows/genetic-variant-annotation/scripts/plot_variant_distribution.py +372 -0
  1082. package/data/workflows/genetic-variant-annotation/scripts/prioritize_variants.py +287 -0
  1083. package/data/workflows/genetic-variant-annotation/scripts/run_snpeff.py +418 -0
  1084. package/data/workflows/genetic-variant-annotation/scripts/run_vep.py +358 -0
  1085. package/data/workflows/genetic-variant-annotation/scripts/select_tool.py +203 -0
  1086. package/data/workflows/genetic-variant-annotation/scripts/test_complete_workflow.py +312 -0
  1087. package/data/workflows/genetic-variant-annotation/scripts/test_pickle_load.py +118 -0
  1088. package/data/workflows/genetic-variant-annotation/scripts/validate_vcf.py +351 -0
  1089. package/data/workflows/genetic-variant-annotation/scripts/verify_changes.py +212 -0
  1090. package/data/workflows/grn-pyscenic/SKILL.md +331 -0
  1091. package/data/workflows/grn-pyscenic/references/cli_interface.md +222 -0
  1092. package/data/workflows/grn-pyscenic/references/database_downloads.md +245 -0
  1093. package/data/workflows/grn-pyscenic/scripts/export_all.py +192 -0
  1094. package/data/workflows/grn-pyscenic/scripts/generate_report.py +512 -0
  1095. package/data/workflows/grn-pyscenic/scripts/integrate_with_adata.py +54 -0
  1096. package/data/workflows/grn-pyscenic/scripts/load_example_data.py +200 -0
  1097. package/data/workflows/grn-pyscenic/scripts/load_expression_data.py +61 -0
  1098. package/data/workflows/grn-pyscenic/scripts/plot_regulon_visualizations.py +263 -0
  1099. package/data/workflows/grn-pyscenic/scripts/run_grn_workflow.py +184 -0
  1100. package/data/workflows/gwas-to-function-twas/SKILL.md +394 -0
  1101. package/data/workflows/gwas-to-function-twas/references/fusion_best_practices.md +120 -0
  1102. package/data/workflows/gwas-to-function-twas/references/installation-guide.md +414 -0
  1103. package/data/workflows/gwas-to-function-twas/references/ldsc_qc_guidelines.md +287 -0
  1104. package/data/workflows/gwas-to-function-twas/references/spredixxcan_best_practices.md +166 -0
  1105. package/data/workflows/gwas-to-function-twas/references/therapeutic_interpretation_guide.md +717 -0
  1106. package/data/workflows/gwas-to-function-twas/references/tissue_reference_guide.md +182 -0
  1107. package/data/workflows/gwas-to-function-twas/references/troubleshooting_guide.md +317 -0
  1108. package/data/workflows/gwas-to-function-twas/references/twas_hub_validation_guide.md +88 -0
  1109. package/data/workflows/gwas-to-function-twas/scripts/colocalization_analysis.py +187 -0
  1110. package/data/workflows/gwas-to-function-twas/scripts/druggability_scoring.py +199 -0
  1111. package/data/workflows/gwas-to-function-twas/scripts/export_results.py +220 -0
  1112. package/data/workflows/gwas-to-function-twas/scripts/integrate_variant_annotation.py +194 -0
  1113. package/data/workflows/gwas-to-function-twas/scripts/interpret_therapeutic_direction.py +418 -0
  1114. package/data/workflows/gwas-to-function-twas/scripts/mendelian_randomization.py +749 -0
  1115. package/data/workflows/gwas-to-function-twas/scripts/multilayer_direction_analysis.py +471 -0
  1116. package/data/workflows/gwas-to-function-twas/scripts/plot_twas_results.py +252 -0
  1117. package/data/workflows/gwas-to-function-twas/scripts/run_fusion.py +155 -0
  1118. package/data/workflows/gwas-to-function-twas/scripts/run_smultixcan.py +102 -0
  1119. package/data/workflows/gwas-to-function-twas/scripts/run_spredixxcan.py +138 -0
  1120. package/data/workflows/gwas-to-function-twas/scripts/select_reference_panel.py +253 -0
  1121. package/data/workflows/gwas-to-function-twas/scripts/validate_gwas_sumstats.py +214 -0
  1122. package/data/workflows/gwas-to-function-twas/scripts/validate_with_twas_hub.py +439 -0
  1123. package/data/workflows/lasso-biomarker-panel/SKILL.md +322 -0
  1124. package/data/workflows/lasso-biomarker-panel/references/decision-guide.md +64 -0
  1125. package/data/workflows/lasso-biomarker-panel/references/lasso-reference.md +110 -0
  1126. package/data/workflows/lasso-biomarker-panel/references/validation-guide.md +105 -0
  1127. package/data/workflows/lasso-biomarker-panel/scripts/biological_interpretation.R +1560 -0
  1128. package/data/workflows/lasso-biomarker-panel/scripts/biomarker_plots.R +350 -0
  1129. package/data/workflows/lasso-biomarker-panel/scripts/export_results.R +1492 -0
  1130. package/data/workflows/lasso-biomarker-panel/scripts/lasso_workflow.R +328 -0
  1131. package/data/workflows/lasso-biomarker-panel/scripts/load_example_data.R +1903 -0
  1132. package/data/workflows/lasso-biomarker-panel/scripts/plotting_helpers.R +78 -0
  1133. package/data/workflows/lasso-biomarker-panel/scripts/prepare_features.R +225 -0
  1134. package/data/workflows/lasso-biomarker-panel/scripts/query_cellxgene.py +107 -0
  1135. package/data/workflows/lasso-biomarker-panel/scripts/validate_external.R +174 -0
  1136. package/data/workflows/literature-preclinical/SKILL.md +276 -0
  1137. package/data/workflows/literature-preclinical/assets/eval/simple_test.py +386 -0
  1138. package/data/workflows/literature-preclinical/references/experiment-extraction-guide.md +147 -0
  1139. package/data/workflows/literature-preclinical/references/full-text-enrichment-guide.md +121 -0
  1140. package/data/workflows/literature-preclinical/references/preclinical-search-guide.md +117 -0
  1141. package/data/workflows/literature-preclinical/scripts/extract_experiments.py +401 -0
  1142. package/data/workflows/literature-preclinical/scripts/generate_plots.R +303 -0
  1143. package/data/workflows/literature-preclinical/scripts/narrative_synthesis.py +653 -0
  1144. package/data/workflows/literature-preclinical/scripts/preclinical_search.py +332 -0
  1145. package/data/workflows/literature-preclinical/scripts/preclinical_synthesis.py +237 -0
  1146. package/data/workflows/literature-preclinical/scripts/report_generation.py +326 -0
  1147. package/data/workflows/mendelian-randomization-twosamplemr/SKILL.md +210 -0
  1148. package/data/workflows/mendelian-randomization-twosamplemr/references/interpretation-guide.md +239 -0
  1149. package/data/workflows/mendelian-randomization-twosamplemr/references/method-reference.md +190 -0
  1150. package/data/workflows/mendelian-randomization-twosamplemr/scripts/export_results.R +123 -0
  1151. package/data/workflows/mendelian-randomization-twosamplemr/scripts/generate_report.R +411 -0
  1152. package/data/workflows/mendelian-randomization-twosamplemr/scripts/load_data.R +281 -0
  1153. package/data/workflows/mendelian-randomization-twosamplemr/scripts/mr_plots.R +163 -0
  1154. package/data/workflows/mendelian-randomization-twosamplemr/scripts/run_mr_analysis.R +322 -0
  1155. package/data/workflows/pcr-primer-design/SKILL.md +397 -0
  1156. package/data/workflows/pcr-primer-design/references/code_examples.md +594 -0
  1157. package/data/workflows/pcr-primer-design/references/miqe_guidelines.md +453 -0
  1158. package/data/workflows/pcr-primer-design/references/parameter_ranges.md +356 -0
  1159. package/data/workflows/pcr-primer-design/references/primer_design_best_practices.md +451 -0
  1160. package/data/workflows/pcr-primer-design/references/troubleshooting_guide.md +477 -0
  1161. package/data/workflows/pcr-primer-design/scripts/__init__.py +2 -0
  1162. package/data/workflows/pcr-primer-design/scripts/calculate_tm.py +306 -0
  1163. package/data/workflows/pcr-primer-design/scripts/check_dimers.py +298 -0
  1164. package/data/workflows/pcr-primer-design/scripts/check_secondary_structures.py +343 -0
  1165. package/data/workflows/pcr-primer-design/scripts/design_qpcr_primers.py +233 -0
  1166. package/data/workflows/pcr-primer-design/scripts/design_standard_primers.py +197 -0
  1167. package/data/workflows/pcr-primer-design/scripts/design_taqman_probes.py +226 -0
  1168. package/data/workflows/pcr-primer-design/scripts/export_results.py +382 -0
  1169. package/data/workflows/pcr-primer-design/scripts/generate_reports.py +379 -0
  1170. package/data/workflows/pcr-primer-design/scripts/validate_specificity.py +311 -0
  1171. package/data/workflows/pcr-primer-design/scripts/visualize_primers.py +379 -0
  1172. package/data/workflows/polygenic-risk-score-prs-catalog/SKILL.md +195 -0
  1173. package/data/workflows/polygenic-risk-score-prs-catalog/references/interpretation-guide.md +80 -0
  1174. package/data/workflows/polygenic-risk-score-prs-catalog/references/pgs-catalog-guide.md +109 -0
  1175. package/data/workflows/polygenic-risk-score-prs-catalog/scripts/export_results.R +186 -0
  1176. package/data/workflows/polygenic-risk-score-prs-catalog/scripts/generate_plots.R +283 -0
  1177. package/data/workflows/polygenic-risk-score-prs-catalog/scripts/load_pgs_weights.R +228 -0
  1178. package/data/workflows/polygenic-risk-score-prs-catalog/scripts/load_reference_data.R +191 -0
  1179. package/data/workflows/polygenic-risk-score-prs-catalog/scripts/score_traits.R +216 -0
  1180. package/data/workflows/pooled-crispr-screens/SKILL.md +362 -0
  1181. package/data/workflows/pooled-crispr-screens/references/crispr_screen_best_practices.md +349 -0
  1182. package/data/workflows/pooled-crispr-screens/references/qc_guidelines.md +722 -0
  1183. package/data/workflows/pooled-crispr-screens/references/statistical_methods.md +644 -0
  1184. package/data/workflows/pooled-crispr-screens/references/troubleshooting_guide.md +684 -0
  1185. package/data/workflows/pooled-crispr-screens/references/umi_optimization.md +297 -0
  1186. package/data/workflows/pooled-crispr-screens/scripts/concatenate_libraries.py +132 -0
  1187. package/data/workflows/pooled-crispr-screens/scripts/detect_perturbed_cells.py +255 -0
  1188. package/data/workflows/pooled-crispr-screens/scripts/differential_expression.py +202 -0
  1189. package/data/workflows/pooled-crispr-screens/scripts/differential_expression_glmgampoi.py +320 -0
  1190. package/data/workflows/pooled-crispr-screens/scripts/export_results.py +261 -0
  1191. package/data/workflows/pooled-crispr-screens/scripts/expression_filtering.py +159 -0
  1192. package/data/workflows/pooled-crispr-screens/scripts/gene_name_corrections.py +188 -0
  1193. package/data/workflows/pooled-crispr-screens/scripts/generate_report.py +485 -0
  1194. package/data/workflows/pooled-crispr-screens/scripts/load_10x_libraries.py +69 -0
  1195. package/data/workflows/pooled-crispr-screens/scripts/load_example_data.py +257 -0
  1196. package/data/workflows/pooled-crispr-screens/scripts/map_sgrna_to_cells.py +119 -0
  1197. package/data/workflows/pooled-crispr-screens/scripts/normalize_and_scale.py +140 -0
  1198. package/data/workflows/pooled-crispr-screens/scripts/qc_filtering.py +185 -0
  1199. package/data/workflows/pooled-crispr-screens/scripts/run_glmgampoi.R +181 -0
  1200. package/data/workflows/pooled-crispr-screens/scripts/screen_all_perturbations.py +306 -0
  1201. package/data/workflows/pooled-crispr-screens/scripts/validate_perturbations.py +314 -0
  1202. package/data/workflows/pooled-crispr-screens/scripts/visualize_perturbations.py +314 -0
  1203. package/data/workflows/scrnaseq-scanpy-core-analysis/SKILL.md +425 -0
  1204. package/data/workflows/scrnaseq-scanpy-core-analysis/references/ambient_rna_correction.md +422 -0
  1205. package/data/workflows/scrnaseq-scanpy-core-analysis/references/common-patterns.md +533 -0
  1206. package/data/workflows/scrnaseq-scanpy-core-analysis/references/integration_methods.md +820 -0
  1207. package/data/workflows/scrnaseq-scanpy-core-analysis/references/marker_gene_database.md +471 -0
  1208. package/data/workflows/scrnaseq-scanpy-core-analysis/references/pseudobulk_de_guide.md +408 -0
  1209. package/data/workflows/scrnaseq-scanpy-core-analysis/references/qc_guidelines.md +535 -0
  1210. package/data/workflows/scrnaseq-scanpy-core-analysis/references/scanpy_best_practices.md +496 -0
  1211. package/data/workflows/scrnaseq-scanpy-core-analysis/references/troubleshooting_guide.md +668 -0
  1212. package/data/workflows/scrnaseq-scanpy-core-analysis/references/workflow-details.md +727 -0
  1213. package/data/workflows/scrnaseq-scanpy-core-analysis/scripts/annotate_celltypes.py +431 -0
  1214. package/data/workflows/scrnaseq-scanpy-core-analysis/scripts/cluster_cells.py +293 -0
  1215. package/data/workflows/scrnaseq-scanpy-core-analysis/scripts/export_results.py +423 -0
  1216. package/data/workflows/scrnaseq-scanpy-core-analysis/scripts/filter_cells.py +531 -0
  1217. package/data/workflows/scrnaseq-scanpy-core-analysis/scripts/find_markers.py +391 -0
  1218. package/data/workflows/scrnaseq-scanpy-core-analysis/scripts/find_variable_genes.py +222 -0
  1219. package/data/workflows/scrnaseq-scanpy-core-analysis/scripts/integrate_scvi.py +665 -0
  1220. package/data/workflows/scrnaseq-scanpy-core-analysis/scripts/integration_diagnostics.py +678 -0
  1221. package/data/workflows/scrnaseq-scanpy-core-analysis/scripts/load_example_data.py +68 -0
  1222. package/data/workflows/scrnaseq-scanpy-core-analysis/scripts/normalize_data.py +325 -0
  1223. package/data/workflows/scrnaseq-scanpy-core-analysis/scripts/plot_dimreduction.py +389 -0
  1224. package/data/workflows/scrnaseq-scanpy-core-analysis/scripts/plot_qc.py +320 -0
  1225. package/data/workflows/scrnaseq-scanpy-core-analysis/scripts/pseudobulk_de.py +553 -0
  1226. package/data/workflows/scrnaseq-scanpy-core-analysis/scripts/qc_metrics.py +477 -0
  1227. package/data/workflows/scrnaseq-scanpy-core-analysis/scripts/remove_ambient_rna.py +347 -0
  1228. package/data/workflows/scrnaseq-scanpy-core-analysis/scripts/run_umap.py +188 -0
  1229. package/data/workflows/scrnaseq-scanpy-core-analysis/scripts/scale_and_pca.py +365 -0
  1230. package/data/workflows/scrnaseq-scanpy-core-analysis/scripts/setup_and_import.py +334 -0
  1231. package/data/workflows/scrnaseq-seurat-core-analysis/SKILL.md +585 -0
  1232. package/data/workflows/scrnaseq-seurat-core-analysis/references/ambient_rna_correction.md +422 -0
  1233. package/data/workflows/scrnaseq-seurat-core-analysis/references/common-patterns.md +667 -0
  1234. package/data/workflows/scrnaseq-seurat-core-analysis/references/decision-guide.md +456 -0
  1235. package/data/workflows/scrnaseq-seurat-core-analysis/references/integration_methods.md +864 -0
  1236. package/data/workflows/scrnaseq-seurat-core-analysis/references/marker_gene_database.md +471 -0
  1237. package/data/workflows/scrnaseq-seurat-core-analysis/references/pseudobulk_de_guide.md +408 -0
  1238. package/data/workflows/scrnaseq-seurat-core-analysis/references/qc_guidelines.md +452 -0
  1239. package/data/workflows/scrnaseq-seurat-core-analysis/references/seurat_best_practices.md +417 -0
  1240. package/data/workflows/scrnaseq-seurat-core-analysis/references/troubleshooting_guide.md +566 -0
  1241. package/data/workflows/scrnaseq-seurat-core-analysis/references/workflow-details.md +801 -0
  1242. package/data/workflows/scrnaseq-seurat-core-analysis/scripts/annotate_celltypes.R +306 -0
  1243. package/data/workflows/scrnaseq-seurat-core-analysis/scripts/cluster_cells.R +223 -0
  1244. package/data/workflows/scrnaseq-seurat-core-analysis/scripts/export_results.R +292 -0
  1245. package/data/workflows/scrnaseq-seurat-core-analysis/scripts/filter_cells.R +576 -0
  1246. package/data/workflows/scrnaseq-seurat-core-analysis/scripts/find_markers.R +325 -0
  1247. package/data/workflows/scrnaseq-seurat-core-analysis/scripts/find_variable_features.R +106 -0
  1248. package/data/workflows/scrnaseq-seurat-core-analysis/scripts/integrate_batches.R +504 -0
  1249. package/data/workflows/scrnaseq-seurat-core-analysis/scripts/integration_diagnostics.R +596 -0
  1250. package/data/workflows/scrnaseq-seurat-core-analysis/scripts/load_example_data.R +89 -0
  1251. package/data/workflows/scrnaseq-seurat-core-analysis/scripts/normalize_data.R +184 -0
  1252. package/data/workflows/scrnaseq-seurat-core-analysis/scripts/plot_dimreduction.R +273 -0
  1253. package/data/workflows/scrnaseq-seurat-core-analysis/scripts/plot_qc.R +250 -0
  1254. package/data/workflows/scrnaseq-seurat-core-analysis/scripts/pseudobulk_de.R +324 -0
  1255. package/data/workflows/scrnaseq-seurat-core-analysis/scripts/qc_metrics.R +358 -0
  1256. package/data/workflows/scrnaseq-seurat-core-analysis/scripts/remove_ambient_rna.R +281 -0
  1257. package/data/workflows/scrnaseq-seurat-core-analysis/scripts/run_umap.R +116 -0
  1258. package/data/workflows/scrnaseq-seurat-core-analysis/scripts/scale_and_pca.R +243 -0
  1259. package/data/workflows/scrnaseq-seurat-core-analysis/scripts/setup_and_import.R +193 -0
  1260. package/data/workflows/spatial-transcriptomics/SKILL.md +256 -0
  1261. package/data/workflows/spatial-transcriptomics/references/spatial-analysis-guide.md +216 -0
  1262. package/data/workflows/spatial-transcriptomics/scripts/export_results.py +214 -0
  1263. package/data/workflows/spatial-transcriptomics/scripts/generate_all_plots.py +397 -0
  1264. package/data/workflows/spatial-transcriptomics/scripts/load_example_data.py +175 -0
  1265. package/data/workflows/spatial-transcriptomics/scripts/spatial_workflow.py +206 -0
  1266. package/dist/bgi.js +128 -2
  1267. package/package.json +2 -1
@@ -0,0 +1,1576 @@
1
+ ---
2
+ name: treatment-plans
3
+ description: "Generate concise (3-4 page), focused medical treatment plans in LaTeX/PDF format for all clinical specialties. Supports general medical treatment, rehabilitation therapy, mental health care, chronic disease management, perioperative care, and pain management. Includes SMART goal frameworks, evidence-based interventions with minimal text citations, regulatory compliance (HIPAA), and professional formatting. Prioritizes brevity and clinical actionability."
4
+ allowed-tools: [Read, Write, Edit, Bash]
5
+ ---
6
+
7
+ # Treatment Plan Writing
8
+
9
+ ## Overview
10
+
11
+ Treatment plan writing is the systematic documentation of clinical care strategies designed to address patient health conditions through evidence-based interventions, measurable goals, and structured follow-up. This skill provides comprehensive LaTeX templates and validation tools for creating **concise, focused** treatment plans (3-4 pages standard) across all medical specialties with full regulatory compliance.
12
+
13
+ **Critical Principles:**
14
+ 1. **CONCISE & ACTIONABLE**: Treatment plans default to 3-4 pages maximum, focusing only on clinically essential information that impacts care decisions
15
+ 2. **Patient-Centered**: Plans must be evidence-based, measurable, and compliant with healthcare regulations (HIPAA, documentation standards)
16
+ 3. **Minimal Citations**: Use brief in-text citations only when needed to support clinical recommendations; avoid extensive bibliographies
17
+
18
+ Every treatment plan should include clear goals, specific interventions, defined timelines, monitoring parameters, and expected outcomes that align with patient preferences and current clinical guidelines - all presented as efficiently as possible.
19
+
20
+ ## When to Use This Skill
21
+
22
+ This skill should be used when:
23
+ - Creating individualized treatment plans for patient care
24
+ - Documenting therapeutic interventions for chronic disease management
25
+ - Developing rehabilitation programs (physical therapy, occupational therapy, cardiac rehab)
26
+ - Writing mental health and psychiatric treatment plans
27
+ - Planning perioperative and surgical care pathways
28
+ - Establishing pain management protocols
29
+ - Setting patient-centered goals using SMART criteria
30
+ - Coordinating multidisciplinary care across specialties
31
+ - Ensuring regulatory compliance in treatment documentation
32
+ - Generating professional treatment plans for medical records
33
+
34
+ ## Visual Enhancement with Scientific Schematics
35
+
36
+ **⚠️ MANDATORY: Every treatment plan MUST include at least 1 AI-generated figure using the scientific-schematics skill.**
37
+
38
+ This is not optional. Treatment plans benefit greatly from visual elements. Before finalizing any document:
39
+ 1. Generate at minimum ONE schematic or diagram (e.g., treatment pathway flowchart, care coordination diagram, or therapy timeline)
40
+ 2. For complex plans: include decision algorithm flowchart
41
+ 3. For rehabilitation plans: include milestone progression diagram
42
+
43
+ **How to generate figures:**
44
+ - Use the **scientific-schematics** skill to generate AI-powered publication-quality diagrams
45
+ - Simply describe your desired diagram in natural language
46
+ - Nano Banana Pro will automatically generate, review, and refine the schematic
47
+
48
+ **How to generate schematics:**
49
+ ```bash
50
+ python scripts/generate_schematic.py "your diagram description" -o figures/output.png
51
+ ```
52
+
53
+ The AI will automatically:
54
+ - Create publication-quality images with proper formatting
55
+ - Review and refine through multiple iterations
56
+ - Ensure accessibility (colorblind-friendly, high contrast)
57
+ - Save outputs in the figures/ directory
58
+
59
+ **When to add schematics:**
60
+ - Treatment pathway flowcharts
61
+ - Care coordination diagrams
62
+ - Therapy progression timelines
63
+ - Multidisciplinary team interaction diagrams
64
+ - Medication management flowcharts
65
+ - Rehabilitation protocol visualizations
66
+ - Clinical decision algorithm diagrams
67
+ - Any complex concept that benefits from visualization
68
+
69
+ For detailed guidance on creating schematics, refer to the scientific-schematics skill documentation.
70
+
71
+ ---
72
+
73
+ ## Document Format and Best Practices
74
+
75
+ ### Document Length Options
76
+
77
+ Treatment plans come in three format options based on clinical complexity and use case:
78
+
79
+ #### Option 1: One-Page Treatment Plan (PREFERRED for most cases)
80
+
81
+ **When to use**: Straightforward clinical scenarios, standard protocols, busy clinical settings
82
+
83
+ **Format**: Single page containing all essential treatment information in scannable sections
84
+ - No table of contents needed
85
+ - No extensive narratives
86
+ - Focused on actionable items only
87
+ - Similar to precision oncology reports or treatment recommendation cards
88
+
89
+ **Required sections** (all on one page):
90
+ 1. **Header Box**: Patient info, diagnosis, date, molecular/risk profile if applicable
91
+ 2. **Treatment Regimen**: Numbered list of specific interventions
92
+ 3. **Supportive Care**: Brief bullet points
93
+ 4. **Rationale**: 1-2 sentence justification (optional for standard protocols)
94
+ 5. **Monitoring**: Key parameters and frequency
95
+ 6. **Evidence Level**: Guideline reference or evidence grade (e.g., "Level 1, FDA approved")
96
+ 7. **Expected Outcome**: Timeline and success metrics
97
+
98
+ **Design principles**:
99
+ - Use small boxes/tables for organization (like the clinical treatment recommendation card format)
100
+ - Eliminate all non-essential text
101
+ - Use abbreviations familiar to clinicians
102
+ - Dense information layout - maximize information per square inch
103
+ - Think "quick reference card" not "comprehensive documentation"
104
+
105
+ **Example structure**:
106
+ ```latex
107
+ [Patient ID/Diagnosis Box at top]
108
+
109
+ TARGET PATIENT POPULATION
110
+ Number of patients, demographics, key features
111
+
112
+ PRIMARY TREATMENT REGIMEN
113
+ • Medication 1: dose, frequency, duration
114
+ • Procedure: specific details
115
+ • Monitoring: what and when
116
+
117
+ SUPPORTIVE CARE
118
+ • Key supportive medications
119
+
120
+ RATIONALE
121
+ Brief clinical justification
122
+
123
+ MOLECULAR TARGETS / RISK FACTORS
124
+ Relevant biomarkers or risk stratification
125
+
126
+ EVIDENCE LEVEL
127
+ Guideline reference, trial data
128
+
129
+ MONITORING REQUIREMENTS
130
+ Key labs/vitals, frequency
131
+
132
+ EXPECTED CLINICAL BENEFIT
133
+ Primary endpoint, timeline
134
+ ```
135
+
136
+ #### Option 2: Standard 3-4 Page Format
137
+
138
+ **When to use**: Moderate complexity, need for patient education materials, multidisciplinary coordination
139
+
140
+ Uses the Foundation Medicine first-page summary model with 2-3 additional pages of details.
141
+
142
+ #### Option 3: Extended 5-6 Page Format
143
+
144
+ **When to use**: Complex comorbidities, research protocols, extensive safety monitoring required
145
+
146
+ ### First Page Summary (Foundation Medicine Model)
147
+
148
+ **CRITICAL REQUIREMENT: All treatment plans MUST have a complete executive summary on the first page ONLY, before any table of contents or detailed sections.**
149
+
150
+ Following the Foundation Medicine model for precision medicine reporting and clinical summary documents, treatment plans begin with a one-page executive summary that provides immediate access to key actionable information. This entire summary must fit on the first page.
151
+
152
+ **Required First Page Structure (in order):**
153
+
154
+ 1. **Title and Subtitle**
155
+ - Main title: Treatment plan type (e.g., "Comprehensive Treatment Plan")
156
+ - Subtitle: Specific condition or focus (e.g., "Type 2 Diabetes Mellitus - Young Adult Patient")
157
+
158
+ 2. **Report Information Box** (using `\begin{infobox}` or `\begin{patientinfo}`)
159
+ - Report type/document purpose
160
+ - Date of plan creation
161
+ - Patient demographics (age, sex, de-identified)
162
+ - Primary diagnosis with ICD-10 code
163
+ - Report author/clinic (if applicable)
164
+ - Analysis approach or framework used
165
+
166
+ 3. **Key Findings or Treatment Highlights** (2-4 colored boxes using appropriate box types)
167
+ - **Primary Treatment Goals** (using `\begin{goalbox}`)
168
+ - 2-3 SMART goals in bullet format
169
+ - **Main Interventions** (using `\begin{keybox}` or `\begin{infobox}`)
170
+ - 2-3 key interventions (pharmacological, non-pharmacological, monitoring)
171
+ - **Critical Decision Points** (using `\begin{warningbox}` if urgent)
172
+ - Important monitoring thresholds or safety considerations
173
+ - **Timeline Overview** (using `\begin{infobox}`)
174
+ - Brief treatment duration/phases
175
+ - Key milestone dates
176
+
177
+ **Visual Format Requirements:**
178
+ - Use `\thispagestyle{empty}` to remove page numbers from first page
179
+ - All content must fit on page 1 (before `\newpage`)
180
+ - Use colored boxes (tcolorbox package) with different colors for different information types
181
+ - Boxes should be visually prominent and easy to scan
182
+ - Use concise, bullet-point format
183
+ - Table of contents (if included) starts on page 2
184
+ - Detailed sections start on page 3
185
+
186
+ **Example First Page Structure:**
187
+ ```latex
188
+ \maketitle
189
+ \thispagestyle{empty}
190
+
191
+ % Report Information Box
192
+ \begin{patientinfo}
193
+ Report Type, Date, Patient Info, Diagnosis, etc.
194
+ \end{patientinfo}
195
+
196
+ % Key Finding #1: Treatment Goals
197
+ \begin{goalbox}[Primary Treatment Goals]
198
+ • Goal 1
199
+ • Goal 2
200
+ • Goal 3
201
+ \end{goalbox}
202
+
203
+ % Key Finding #2: Main Interventions
204
+ \begin{keybox}[Core Interventions]
205
+ • Intervention 1
206
+ • Intervention 2
207
+ • Intervention 3
208
+ \end{keybox}
209
+
210
+ % Key Finding #3: Critical Monitoring (if applicable)
211
+ \begin{warningbox}[Critical Decision Points]
212
+ • Decision point 1
213
+ • Decision point 2
214
+ \end{warningbox}
215
+
216
+ \newpage
217
+ \tableofcontents % TOC on page 2
218
+ \newpage % Detailed content starts page 3
219
+ ```
220
+
221
+ ### Concise Documentation
222
+
223
+ **CRITICAL: Treatment plans MUST prioritize brevity and clinical relevance. Default to 3-4 pages maximum unless clinical complexity absolutely demands more detail.**
224
+
225
+ Treatment plans should prioritize **clarity and actionability** over exhaustive detail:
226
+
227
+ - **Focused**: Include only clinically essential information that impacts care decisions
228
+ - **Actionable**: Emphasize what needs to be done, when, and why
229
+ - **Efficient**: Facilitate quick decision-making without sacrificing clinical quality
230
+ - **Target length options**:
231
+ - **1-page format** (preferred for straightforward cases): Quick-reference card with all essential information
232
+ - **3-4 pages standard**: Standard format with first-page summary + supporting details
233
+ - **5-6 pages** (rare): Only for highly complex cases with multiple comorbidities or multidisciplinary interventions
234
+
235
+ **Streamlining Guidelines:**
236
+ - **First Page Summary**: Use individual colored boxes to consolidate key information (goals, interventions, decision points) - this alone can often convey the essential treatment plan
237
+ - **Eliminate Redundancy**: If information is in the first-page summary, don't repeat it verbatim in detailed sections
238
+ - **Patient Education section**: 3-5 key bullet points on critical topics and warning signs only
239
+ - **Risk Mitigation section**: Highlight only critical medication safety concerns and emergency actions (not exhaustive lists)
240
+ - **Expected Outcomes section**: 2-3 concise statements on anticipated responses and timelines
241
+ - **Interventions**: Focus on primary interventions; secondary/supportive measures in brief bullet format
242
+ - **Use tables and bullet points** extensively for efficient presentation
243
+ - **Avoid narrative prose** where structured lists suffice
244
+ - **Combine related sections** when appropriate to reduce page count
245
+
246
+ ### Quality Over Quantity
247
+
248
+ The goal is professional, clinically complete documentation that respects clinicians' time while ensuring comprehensive patient care. Every section should add value; remove or condense sections that don't directly inform treatment decisions.
249
+
250
+ ### Citations and Evidence Support
251
+
252
+ **Use minimal, targeted citations to support clinical recommendations:**
253
+
254
+ - **Text Citations Preferred**: Use brief in-text citations (Author Year) or simple references rather than extensive bibliographies unless specifically requested
255
+ - **When to Cite**:
256
+ - Clinical practice guideline recommendations (e.g., "per ADA 2024 guidelines")
257
+ - Specific medication dosing or protocols (e.g., "ACC/AHA recommendations")
258
+ - Novel or controversial interventions requiring evidence support
259
+ - Risk stratification tools or validated assessment scales
260
+ - **When NOT to Cite**:
261
+ - Standard-of-care interventions widely accepted in the field
262
+ - Basic medical facts and routine clinical practices
263
+ - General patient education content
264
+ - **Citation Format**:
265
+ - Inline: "Initiate metformin as first-line therapy (ADA Standards of Care 2024)"
266
+ - Minimal: "Treatment follows ACC/AHA heart failure guidelines"
267
+ - Avoid formal numbered references and extensive bibliography sections unless document is for academic/research purposes
268
+ - **Keep it Brief**: A 3-4 page treatment plan should have 0-3 citations maximum, only where essential for clinical credibility or novel recommendations
269
+
270
+ ## Core Capabilities
271
+
272
+ ### 1. General Medical Treatment Plans
273
+
274
+ General medical treatment plans address common chronic conditions and acute medical issues requiring structured therapeutic interventions.
275
+
276
+ #### Standard Components
277
+
278
+ **Patient Information (De-identified)**
279
+ - Demographics (age, sex, relevant medical background)
280
+ - Active medical conditions and comorbidities
281
+ - Current medications and allergies
282
+ - Relevant social and family history
283
+ - Functional status and baseline assessments
284
+ - **HIPAA Compliance**: Remove all 18 identifiers per Safe Harbor method
285
+
286
+ **Diagnosis and Assessment Summary**
287
+ - Primary diagnosis with ICD-10 code
288
+ - Secondary diagnoses and comorbidities
289
+ - Severity classification and staging
290
+ - Functional limitations and quality of life impact
291
+ - Risk stratification (e.g., cardiovascular risk, fall risk)
292
+ - Prognostic indicators
293
+
294
+ **Treatment Goals (SMART Format)**
295
+
296
+ Short-term goals (1-3 months):
297
+ - **Specific**: Clearly defined outcome (e.g., "Reduce HbA1c to <7%")
298
+ - **Measurable**: Quantifiable metrics (e.g., "Decrease systolic BP by 10 mmHg")
299
+ - **Achievable**: Realistic given patient capabilities
300
+ - **Relevant**: Aligned with patient priorities and values
301
+ - **Time-bound**: Specific timeframe (e.g., "within 8 weeks")
302
+
303
+ Long-term goals (6-12 months):
304
+ - Disease control or remission targets
305
+ - Functional improvement objectives
306
+ - Quality of life enhancement
307
+ - Prevention of complications
308
+ - Maintenance of independence
309
+
310
+ **Interventions**
311
+
312
+ *Pharmacological*:
313
+ - Medications with specific dosages, routes, frequencies
314
+ - Titration schedules and target doses
315
+ - Drug-drug interaction considerations
316
+ - Monitoring for adverse effects
317
+ - Medication reconciliation
318
+
319
+ *Non-pharmacological*:
320
+ - Lifestyle modifications (diet, exercise, smoking cessation)
321
+ - Behavioral interventions
322
+ - Patient education and self-management
323
+ - Monitoring and self-tracking (glucose, blood pressure, weight)
324
+ - Assistive devices or adaptive equipment
325
+
326
+ *Procedural*:
327
+ - Planned procedures or interventions
328
+ - Referrals to specialists
329
+ - Diagnostic testing schedule
330
+ - Preventive care (vaccinations, screenings)
331
+
332
+ **Timeline and Schedule**
333
+ - Treatment phases with specific timeframes
334
+ - Appointment frequency (weekly, monthly, quarterly)
335
+ - Milestone assessments and goal evaluations
336
+ - Medication adjustments schedule
337
+ - Expected duration of treatment
338
+
339
+ **Monitoring Parameters**
340
+ - Clinical outcomes to track (vital signs, lab values, symptoms)
341
+ - Assessment tools and scales (e.g., PHQ-9, pain scales)
342
+ - Frequency of monitoring
343
+ - Thresholds for intervention or escalation
344
+ - Patient-reported outcomes
345
+
346
+ **Expected Outcomes**
347
+ - Primary outcome measures
348
+ - Success criteria and benchmarks
349
+ - Expected timeline for improvement
350
+ - Criteria for treatment modification
351
+ - Long-term prognosis
352
+
353
+ **Follow-up Plan**
354
+ - Scheduled appointments and reassessments
355
+ - Communication plan (phone calls, secure messaging)
356
+ - Emergency contact procedures
357
+ - Criteria for urgent evaluation
358
+ - Transition or discharge planning
359
+
360
+ **Patient Education**
361
+ - Understanding of condition and treatment rationale
362
+ - Self-management skills training
363
+ - Medication administration and adherence
364
+ - Warning signs and when to seek help
365
+ - Resources and support services
366
+
367
+ **Risk Mitigation**
368
+ - Potential adverse effects and management
369
+ - Drug interactions and contraindications
370
+ - Fall prevention, infection prevention
371
+ - Emergency action plans
372
+ - Safety monitoring
373
+
374
+ #### Common Applications
375
+
376
+ - Diabetes mellitus management
377
+ - Hypertension control
378
+ - Heart failure treatment
379
+ - COPD management
380
+ - Asthma care plans
381
+ - Hyperlipidemia treatment
382
+ - Osteoarthritis management
383
+ - Chronic kidney disease
384
+
385
+ ### 2. Rehabilitation Treatment Plans
386
+
387
+ Rehabilitation plans focus on restoring function, improving mobility, and enhancing quality of life through structured therapeutic programs.
388
+
389
+ #### Core Components
390
+
391
+ **Functional Assessment**
392
+ - Baseline functional status (ADLs, IADLs)
393
+ - Range of motion, strength, balance, endurance
394
+ - Gait analysis and mobility assessment
395
+ - Standardized measures (FIM, Barthel Index, Berg Balance Scale)
396
+ - Environmental assessment (home safety, accessibility)
397
+
398
+ **Rehabilitation Goals**
399
+
400
+ *Impairment-level goals*:
401
+ - Improve shoulder flexion to 140 degrees
402
+ - Increase quadriceps strength by 2/5 MMT grades
403
+ - Enhance balance (Berg Score >45/56)
404
+
405
+ *Activity-level goals*:
406
+ - Independent ambulation 150 feet with assistive device
407
+ - Climb 12 stairs with handrail supervision
408
+ - Transfer bed-to-chair independently
409
+
410
+ *Participation-level goals*:
411
+ - Return to work with modifications
412
+ - Resume recreational activities
413
+ - Independent community mobility
414
+
415
+ **Therapeutic Interventions**
416
+
417
+ *Physical Therapy*:
418
+ - Therapeutic exercises (strengthening, stretching, endurance)
419
+ - Manual therapy techniques
420
+ - Gait training and balance activities
421
+ - Modalities (heat, ice, electrical stimulation, ultrasound)
422
+ - Assistive device training
423
+
424
+ *Occupational Therapy*:
425
+ - ADL training (bathing, dressing, grooming, feeding)
426
+ - Upper extremity strengthening and coordination
427
+ - Adaptive equipment and modifications
428
+ - Energy conservation techniques
429
+ - Cognitive rehabilitation
430
+
431
+ *Speech-Language Pathology*:
432
+ - Swallowing therapy and dysphagia management
433
+ - Communication strategies and augmentative devices
434
+ - Cognitive-linguistic therapy
435
+ - Voice therapy
436
+
437
+ *Other Services*:
438
+ - Recreational therapy
439
+ - Aquatic therapy
440
+ - Cardiac rehabilitation
441
+ - Pulmonary rehabilitation
442
+ - Vestibular rehabilitation
443
+
444
+ **Treatment Schedule**
445
+ - Frequency: 3x/week PT, 2x/week OT (example)
446
+ - Session duration: 45-60 minutes
447
+ - Treatment phase durations (acute, subacute, maintenance)
448
+ - Expected total duration: 8-12 weeks
449
+ - Reassessment intervals
450
+
451
+ **Progress Monitoring**
452
+ - Weekly functional assessments
453
+ - Standardized outcome measures
454
+ - Goal attainment scaling
455
+ - Pain and symptom tracking
456
+ - Patient satisfaction
457
+
458
+ **Home Exercise Program**
459
+ - Specific exercises with repetitions/sets/frequency
460
+ - Precautions and safety instructions
461
+ - Progression criteria
462
+ - Self-monitoring strategies
463
+
464
+ #### Specialty Rehabilitation
465
+
466
+ - Post-stroke rehabilitation
467
+ - Orthopedic rehabilitation (joint replacement, fracture)
468
+ - Cardiac rehabilitation (post-MI, post-surgery)
469
+ - Pulmonary rehabilitation
470
+ - Vestibular rehabilitation
471
+ - Neurological rehabilitation
472
+ - Sports injury rehabilitation
473
+
474
+ ### 3. Mental Health Treatment Plans
475
+
476
+ Mental health treatment plans address psychiatric conditions through integrated psychotherapeutic, pharmacological, and psychosocial interventions.
477
+
478
+ #### Essential Components
479
+
480
+ **Psychiatric Assessment**
481
+ - Primary psychiatric diagnosis (DSM-5 criteria)
482
+ - Symptom severity and functional impairment
483
+ - Co-occurring mental health conditions
484
+ - Substance use assessment
485
+ - Suicide/homicide risk assessment
486
+ - Trauma history and PTSD screening
487
+ - Social determinants of mental health
488
+
489
+ **Treatment Goals**
490
+
491
+ *Symptom reduction*:
492
+ - Decrease depression severity (PHQ-9 score from 18 to <10)
493
+ - Reduce anxiety symptoms (GAD-7 score <5)
494
+ - Improve sleep quality (Pittsburgh Sleep Quality Index)
495
+ - Stabilize mood (reduced mood episodes)
496
+
497
+ *Functional improvement*:
498
+ - Return to work or school
499
+ - Improve social relationships and support
500
+ - Enhance coping skills and emotional regulation
501
+ - Increase engagement in meaningful activities
502
+
503
+ *Recovery-oriented goals*:
504
+ - Build resilience and self-efficacy
505
+ - Develop crisis management skills
506
+ - Establish sustainable wellness routines
507
+ - Achieve personal recovery goals
508
+
509
+ **Therapeutic Interventions**
510
+
511
+ *Psychotherapy*:
512
+ - Evidence-based modality (CBT, DBT, ACT, psychodynamic, IPT)
513
+ - Session frequency (weekly, biweekly)
514
+ - Treatment duration (12-16 weeks, ongoing)
515
+ - Specific techniques and targets
516
+ - Group therapy participation
517
+
518
+ *Psychopharmacology*:
519
+ - Medication class and rationale
520
+ - Starting dose and titration schedule
521
+ - Target symptoms
522
+ - Expected response timeline (2-4 weeks for antidepressants)
523
+ - Side effect monitoring
524
+ - Combination therapy considerations
525
+
526
+ *Psychosocial Interventions*:
527
+ - Case management services
528
+ - Peer support programs
529
+ - Family therapy or psychoeducation
530
+ - Vocational rehabilitation
531
+ - Supported housing or community integration
532
+ - Substance abuse treatment
533
+
534
+ **Safety Planning**
535
+ - Crisis contacts and emergency services
536
+ - Warning signs and triggers
537
+ - Coping strategies and self-soothing techniques
538
+ - Safe environment modifications
539
+ - Means restriction (firearms, medications)
540
+ - Support system activation
541
+
542
+ **Monitoring and Assessment**
543
+ - Symptom rating scales (weekly or biweekly)
544
+ - Medication adherence and side effects
545
+ - Suicidal ideation screening
546
+ - Functional status assessments
547
+ - Treatment engagement and therapeutic alliance
548
+
549
+ **Patient and Family Education**
550
+ - Psychoeducation about diagnosis
551
+ - Treatment rationale and expectations
552
+ - Medication information
553
+ - Relapse prevention strategies
554
+ - Community resources
555
+
556
+ #### Mental Health Conditions
557
+
558
+ - Major depressive disorder
559
+ - Anxiety disorders (GAD, panic, social anxiety)
560
+ - Bipolar disorder
561
+ - Schizophrenia and psychotic disorders
562
+ - PTSD and trauma-related disorders
563
+ - Eating disorders
564
+ - Substance use disorders
565
+ - Personality disorders
566
+
567
+ ### 4. Chronic Disease Management Plans
568
+
569
+ Comprehensive long-term care plans for chronic conditions requiring ongoing monitoring, treatment adjustments, and multidisciplinary coordination.
570
+
571
+ #### Key Features
572
+
573
+ **Disease-Specific Targets**
574
+ - Evidence-based treatment goals per guidelines
575
+ - Stage-appropriate interventions
576
+ - Complication prevention strategies
577
+ - Disease progression monitoring
578
+
579
+ **Self-Management Support**
580
+ - Patient activation and engagement
581
+ - Shared decision-making
582
+ - Action plans for symptom changes
583
+ - Technology-enabled monitoring (apps, remote monitoring)
584
+
585
+ **Care Coordination**
586
+ - Primary care physician oversight
587
+ - Specialist consultations and co-management
588
+ - Care transitions (hospital to home)
589
+ - Medication management across providers
590
+ - Communication protocols
591
+
592
+ **Population Health Integration**
593
+ - Registry tracking and outreach
594
+ - Preventive care and screening schedules
595
+ - Quality measure reporting
596
+ - Care gaps identification
597
+
598
+ #### Applicable Conditions
599
+
600
+ - Type 1 and Type 2 diabetes
601
+ - Cardiovascular disease (CHF, CAD)
602
+ - Chronic respiratory diseases (COPD, asthma)
603
+ - Chronic kidney disease
604
+ - Inflammatory bowel disease
605
+ - Rheumatoid arthritis and autoimmune conditions
606
+ - HIV/AIDS
607
+ - Cancer survivorship care
608
+
609
+ ### 5. Perioperative Care Plans
610
+
611
+ Structured plans for surgical and procedural patients covering preoperative preparation, intraoperative management, and postoperative recovery.
612
+
613
+ #### Components
614
+
615
+ **Preoperative Assessment**
616
+ - Surgical indication and planned procedure
617
+ - Preoperative risk stratification (ASA class, cardiac risk)
618
+ - Optimization of medical conditions
619
+ - Medication management (continuation, discontinuation)
620
+ - Preoperative testing and clearances
621
+ - Informed consent and patient education
622
+
623
+ **Perioperative Interventions**
624
+ - Enhanced recovery after surgery (ERAS) protocols
625
+ - Venous thromboembolism prophylaxis
626
+ - Antibiotic prophylaxis
627
+ - Glycemic control strategies
628
+ - Pain management plan (multimodal analgesia)
629
+
630
+ **Postoperative Care**
631
+ - Immediate recovery goals (24-48 hours)
632
+ - Early mobilization protocols
633
+ - Diet advancement
634
+ - Wound care and drain management
635
+ - Pain control regimen
636
+ - Complication monitoring
637
+
638
+ **Discharge Planning**
639
+ - Activity restrictions and progression
640
+ - Medication reconciliation
641
+ - Follow-up appointments
642
+ - Home health or rehabilitation services
643
+ - Return-to-work timeline
644
+
645
+ ### 6. Pain Management Plans
646
+
647
+ Multimodal approaches to acute and chronic pain using evidence-based interventions and opioid-sparing strategies.
648
+
649
+ #### Comprehensive Components
650
+
651
+ **Pain Assessment**
652
+ - Pain location, quality, intensity (0-10 scale)
653
+ - Temporal pattern (constant, intermittent, breakthrough)
654
+ - Aggravating and alleviating factors
655
+ - Functional impact (sleep, activities, mood)
656
+ - Previous treatments and responses
657
+ - Psychosocial contributors
658
+
659
+ **Multimodal Interventions**
660
+
661
+ *Pharmacological*:
662
+ - Non-opioid analgesics (acetaminophen, NSAIDs)
663
+ - Adjuvant medications (antidepressants, anticonvulsants, muscle relaxants)
664
+ - Topical agents (lidocaine, capsaicin, diclofenac)
665
+ - Opioid therapy (when appropriate, with risk mitigation)
666
+ - Titration and rotation strategies
667
+
668
+ *Interventional Procedures*:
669
+ - Nerve blocks and injections
670
+ - Radiofrequency ablation
671
+ - Spinal cord stimulation
672
+ - Intrathecal drug delivery
673
+
674
+ *Non-pharmacological*:
675
+ - Physical therapy and exercise
676
+ - Cognitive-behavioral therapy for pain
677
+ - Mindfulness and relaxation techniques
678
+ - Acupuncture
679
+ - TENS units
680
+
681
+ **Opioid Safety (when prescribed)**
682
+ - Indication and planned duration
683
+ - Prescription drug monitoring program (PDMP) check
684
+ - Opioid risk assessment tools
685
+ - Naloxone prescription
686
+ - Treatment agreements
687
+ - Random urine drug screening
688
+ - Frequent follow-up and reassessment
689
+
690
+ **Functional Goals**
691
+ - Specific activity improvements
692
+ - Sleep quality enhancement
693
+ - Reduced pain interference
694
+ - Improved quality of life
695
+ - Return to work or meaningful activities
696
+
697
+ ## Best Practices
698
+
699
+ ### Brevity and Focus (HIGHEST PRIORITY)
700
+
701
+ **Treatment plans MUST be concise and focused on actionable clinical information:**
702
+
703
+ - **1-page format is PREFERRED**: For most clinical scenarios, a single-page treatment plan (like precision oncology reports) provides all necessary information
704
+ - **Default to shortest format possible**: Start with 1-page; only expand if clinical complexity genuinely requires it
705
+ - **Every sentence must add value**: If a section doesn't change clinical decision-making, omit it entirely
706
+ - **Think "quick reference card" not "comprehensive textbook"**: Busy clinicians need scannable, dense information
707
+ - **Avoid academic verbosity**: This is clinical documentation, not a literature review or teaching document
708
+ - **Maximum lengths by complexity**:
709
+ - Simple/standard cases: 1 page
710
+ - Moderate complexity: 3-4 pages (first-page summary + details)
711
+ - High complexity (rare): 5-6 pages maximum
712
+
713
+ ### First Page Summary (Most Important)
714
+
715
+ **ALWAYS create a one-page executive summary as the first page:**
716
+ - The first page must contain ONLY: Title, Report Info Box, and Key Findings boxes
717
+ - This provides an at-a-glance overview similar to precision medicine reports
718
+ - Table of contents and detailed sections start on page 2 or later
719
+ - Think of it as a "clinical highlights" page that a busy clinician can scan in 30 seconds
720
+ - Use 2-4 colored boxes for different key findings (goals, interventions, decision points)
721
+ - **A strong first page can often stand alone** - subsequent pages are for details, not repetition
722
+
723
+ ### SMART Goal Setting
724
+
725
+ All treatment goals should meet SMART criteria:
726
+
727
+ - **Specific**: "Improve HbA1c to <7%" not "Better diabetes control"
728
+ - **Measurable**: Use quantifiable metrics, validated scales, objective measures
729
+ - **Achievable**: Consider patient capabilities, resources, social support
730
+ - **Relevant**: Align with patient values, priorities, and life circumstances
731
+ - **Time-bound**: Define clear timeframes for goal achievement and reassessment
732
+
733
+ ### Patient-Centered Care
734
+
735
+ ✓ **Shared Decision-Making**: Involve patients in goal-setting and treatment choices
736
+ ✓ **Cultural Competence**: Respect cultural beliefs, language preferences, health literacy
737
+ ✓ **Patient Preferences**: Honor treatment preferences and personal values
738
+ ✓ **Individualization**: Tailor plans to patient's unique circumstances
739
+ ✓ **Empowerment**: Support patient activation and self-management
740
+
741
+ ### Evidence-Based Practice
742
+
743
+ ✓ **Clinical Guidelines**: Follow current specialty society recommendations
744
+ ✓ **Quality Measures**: Incorporate HEDIS, CMS quality measures
745
+ ✓ **Comparative Effectiveness**: Use treatments with proven efficacy
746
+ ✓ **Avoid Low-Value Care**: Eliminate unnecessary tests and interventions
747
+ ✓ **Stay Current**: Update plans based on emerging evidence
748
+
749
+ ### Documentation Standards
750
+
751
+ ✓ **Completeness**: Include all required elements
752
+ ✓ **Clarity**: Use clear, professional medical language
753
+ ✓ **Accuracy**: Ensure factual correctness and current information
754
+ ✓ **Timeliness**: Document plans promptly
755
+ ✓ **Legibility**: Professional formatting and organization
756
+ ✓ **Signature and Date**: Authenticate all treatment plans
757
+
758
+ ### Regulatory Compliance
759
+
760
+ ✓ **HIPAA Privacy**: De-identify all protected health information
761
+ ✓ **Informed Consent**: Document patient understanding and agreement
762
+ ✓ **Billing Support**: Include documentation to support medical necessity
763
+ ✓ **Quality Reporting**: Enable extraction of quality metrics
764
+ ✓ **Legal Protection**: Maintain defensible clinical documentation
765
+
766
+ ### Multidisciplinary Coordination
767
+
768
+ ✓ **Team Communication**: Share plans across care team
769
+ ✓ **Role Clarity**: Define responsibilities for each team member
770
+ ✓ **Care Transitions**: Ensure continuity across settings
771
+ ✓ **Specialist Integration**: Coordinate with subspecialty care
772
+ ✓ **Patient-Centered Medical Home**: Align with PCMH principles
773
+
774
+ ## LaTeX Template Usage
775
+
776
+ ### Template Selection
777
+
778
+ Choose the appropriate template based on clinical context and desired length:
779
+
780
+ #### Concise Templates (PREFERRED)
781
+
782
+ 1. **one_page_treatment_plan.tex** - **FIRST CHOICE** for most cases
783
+ - All clinical specialties
784
+ - Standard protocols and straightforward cases
785
+ - Quick-reference format similar to precision oncology reports
786
+ - Dense, scannable, clinician-focused
787
+ - Use this unless complexity demands more detail
788
+
789
+ #### Standard Templates (3-4 pages)
790
+
791
+ Use only when one-page format is insufficient due to complexity:
792
+
793
+ 2. **general_medical_treatment_plan.tex** - Primary care, chronic disease, general medicine
794
+ 3. **rehabilitation_treatment_plan.tex** - PT/OT, post-surgery, injury recovery
795
+ 4. **mental_health_treatment_plan.tex** - Psychiatric conditions, behavioral health
796
+ 5. **chronic_disease_management_plan.tex** - Complex chronic diseases, multiple conditions
797
+ 6. **perioperative_care_plan.tex** - Surgical patients, procedural care
798
+ 7. **pain_management_plan.tex** - Acute or chronic pain conditions
799
+
800
+ **Note**: Even when using standard templates, adapt them to be concise (3-4 pages max) by removing non-essential sections.
801
+
802
+ ### Template Structure
803
+
804
+ All LaTeX templates include:
805
+ - Professional formatting with appropriate margins and fonts
806
+ - Structured sections for all required components
807
+ - Tables for medications, interventions, timelines
808
+ - Goal-tracking sections with SMART criteria
809
+ - Space for provider signatures and dates
810
+ - HIPAA-compliant de-identification guidance
811
+ - Comments with detailed instructions
812
+
813
+ ### Generating PDFs
814
+
815
+ ```bash
816
+ # Compile LaTeX template to PDF
817
+ pdflatex general_medical_treatment_plan.tex
818
+
819
+ # For templates with references
820
+ pdflatex treatment_plan.tex
821
+ bibtex treatment_plan
822
+ pdflatex treatment_plan.tex
823
+ pdflatex treatment_plan.tex
824
+ ```
825
+
826
+ ## Validation and Quality Assurance
827
+
828
+ ### Completeness Checking
829
+
830
+ Use validation scripts to ensure all required sections are present:
831
+
832
+ ```bash
833
+ python check_completeness.py my_treatment_plan.tex
834
+ ```
835
+
836
+ The script checks for:
837
+ - Patient information section
838
+ - Diagnosis and assessment
839
+ - SMART goals (short-term and long-term)
840
+ - Interventions (pharmacological, non-pharmacological)
841
+ - Timeline and schedule
842
+ - Monitoring parameters
843
+ - Expected outcomes
844
+ - Follow-up plan
845
+ - Patient education
846
+ - Risk mitigation
847
+
848
+ ### Treatment Plan Validation
849
+
850
+ Comprehensive validation of treatment plan quality:
851
+
852
+ ```bash
853
+ python validate_treatment_plan.py my_treatment_plan.tex
854
+ ```
855
+
856
+ Validation includes:
857
+ - SMART goal criteria assessment
858
+ - Evidence-based intervention verification
859
+ - Timeline feasibility check
860
+ - Monitoring parameter adequacy
861
+ - Safety and risk mitigation review
862
+ - Regulatory compliance check
863
+
864
+ ### Quality Checklist
865
+
866
+ Review treatment plans against the quality checklist (`quality_checklist.md`):
867
+
868
+ **Clinical Quality**
869
+ - [ ] Diagnosis is accurate and properly coded (ICD-10)
870
+ - [ ] Goals are SMART and patient-centered
871
+ - [ ] Interventions are evidence-based and guideline-concordant
872
+ - [ ] Timeline is realistic and clearly defined
873
+ - [ ] Monitoring plan is comprehensive
874
+ - [ ] Safety considerations are addressed
875
+
876
+ **Patient-Centered Care**
877
+ - [ ] Patient preferences and values incorporated
878
+ - [ ] Shared decision-making documented
879
+ - [ ] Health literacy appropriate language
880
+ - [ ] Cultural considerations addressed
881
+ - [ ] Patient education plan included
882
+
883
+ **Regulatory Compliance**
884
+ - [ ] HIPAA-compliant de-identification
885
+ - [ ] Medical necessity documented
886
+ - [ ] Informed consent noted
887
+ - [ ] Provider signature and credentials
888
+ - [ ] Date of plan creation/revision
889
+
890
+ **Coordination and Communication**
891
+ - [ ] Specialist referrals documented
892
+ - [ ] Care team roles defined
893
+ - [ ] Follow-up schedule clear
894
+ - [ ] Emergency contacts provided
895
+ - [ ] Transition planning addressed
896
+
897
+ ## Integration with Other Skills
898
+
899
+ ### Clinical Reports Integration
900
+
901
+ Treatment plans often accompany other clinical documentation:
902
+
903
+ - **SOAP Notes** (`clinical-reports` skill): Document ongoing implementation
904
+ - **H&P** (`clinical-reports` skill): Initial assessment informs treatment plan
905
+ - **Discharge Summaries** (`clinical-reports` skill): Summarize treatment plan execution
906
+ - **Progress Notes**: Track goal achievement and plan modifications
907
+
908
+ ### Scientific Writing Integration
909
+
910
+ Evidence-based treatment planning requires literature support:
911
+
912
+ - **Citation Management** (`citation-management` skill): Reference clinical guidelines
913
+ - **Literature Review** (`literature-review` skill): Understand treatment evidence base
914
+ - **Research Lookup** (`research-lookup` skill): Find current best practices
915
+
916
+ ### Research Integration
917
+
918
+ Treatment plans may be developed for clinical trials or research studies:
919
+
920
+ - **Research Grants** (`research-grants` skill): Treatment protocols for funded studies
921
+ - **Clinical Trial Reports** (`clinical-reports` skill): Intervention documentation
922
+
923
+ ## Common Use Cases
924
+
925
+ ### Example 1: Type 2 Diabetes Management
926
+
927
+ **Scenario**: 58-year-old patient with newly diagnosed Type 2 diabetes, HbA1c 8.5%, BMI 32
928
+
929
+ **Template**: `general_medical_treatment_plan.tex`
930
+
931
+ **Goals**:
932
+ - Short-term: Reduce HbA1c to <7.5% in 3 months
933
+ - Long-term: Achieve HbA1c <7%, lose 15 pounds in 6 months
934
+
935
+ **Interventions**:
936
+ - Pharmacological: Metformin 500mg BID, titrate to 1000mg BID
937
+ - Lifestyle: Mediterranean diet, 150 min/week moderate exercise
938
+ - Education: Diabetes self-management education, glucose monitoring
939
+
940
+ ### Example 2: Post-Stroke Rehabilitation
941
+
942
+ **Scenario**: 70-year-old patient s/p left MCA stroke with right hemiparesis
943
+
944
+ **Template**: `rehabilitation_treatment_plan.tex`
945
+
946
+ **Goals**:
947
+ - Short-term: Improve right arm strength 2/5 to 3/5 in 4 weeks
948
+ - Long-term: Independent ambulation 150 feet with cane in 12 weeks
949
+
950
+ **Interventions**:
951
+ - PT 3x/week: Gait training, balance, strengthening
952
+ - OT 3x/week: ADL training, upper extremity function
953
+ - SLP 2x/week: Dysphagia therapy
954
+
955
+ ### Example 3: Major Depressive Disorder
956
+
957
+ **Scenario**: 35-year-old with moderate depression, PHQ-9 score 16
958
+
959
+ **Template**: `mental_health_treatment_plan.tex`
960
+
961
+ **Goals**:
962
+ - Short-term: Reduce PHQ-9 to <10 in 8 weeks
963
+ - Long-term: Achieve remission (PHQ-9 <5), return to work
964
+
965
+ **Interventions**:
966
+ - Psychotherapy: CBT weekly sessions
967
+ - Medication: Sertraline 50mg daily, titrate to 100mg
968
+ - Lifestyle: Sleep hygiene, exercise 30 min 5x/week
969
+
970
+ ### Example 4: Total Knee Arthroplasty
971
+
972
+ **Scenario**: 68-year-old scheduled for right TKA for osteoarthritis
973
+
974
+ **Template**: `perioperative_care_plan.tex`
975
+
976
+ **Preoperative Goals**:
977
+ - Optimize diabetes control (glucose <180)
978
+ - Discontinue anticoagulation per protocol
979
+ - Complete medical clearance
980
+
981
+ **Postoperative Goals**:
982
+ - Ambulate 50 feet by POD 1
983
+ - 90-degree knee flexion by POD 3
984
+ - Discharge home with PT services by POD 2-3
985
+
986
+ ### Example 5: Chronic Low Back Pain
987
+
988
+ **Scenario**: 45-year-old with chronic non-specific low back pain, pain 7/10
989
+
990
+ **Template**: `pain_management_plan.tex`
991
+
992
+ **Goals**:
993
+ - Short-term: Reduce pain to 4/10 in 6 weeks
994
+ - Long-term: Return to work full-time, pain 2-3/10
995
+
996
+ **Interventions**:
997
+ - Pharmacological: Gabapentin 300mg TID, duloxetine 60mg daily
998
+ - PT: Core strengthening, McKenzie exercises 2x/week x 8 weeks
999
+ - Behavioral: CBT for pain, mindfulness meditation
1000
+ - Interventional: Consider lumbar ESI if inadequate response
1001
+
1002
+ ## Professional Standards and Guidelines
1003
+
1004
+ Treatment plans should align with:
1005
+
1006
+ ### General Medicine
1007
+ - American Diabetes Association (ADA) Standards of Care
1008
+ - ACC/AHA Cardiovascular Guidelines
1009
+ - GOLD COPD Guidelines
1010
+ - JNC-8 Hypertension Guidelines
1011
+ - KDIGO Chronic Kidney Disease Guidelines
1012
+
1013
+ ### Rehabilitation
1014
+ - APTA Clinical Practice Guidelines
1015
+ - AOTA Practice Guidelines
1016
+ - Cardiac Rehabilitation Guidelines (AHA/AACVPR)
1017
+ - Stroke Rehabilitation Guidelines
1018
+
1019
+ ### Mental Health
1020
+ - APA Practice Guidelines
1021
+ - VA/DoD Clinical Practice Guidelines
1022
+ - NICE Guidelines (National Institute for Health and Care Excellence)
1023
+ - Cochrane Reviews for psychiatric interventions
1024
+
1025
+ ### Pain Management
1026
+ - CDC Opioid Prescribing Guidelines
1027
+ - AAPM/APS Chronic Pain Guidelines
1028
+ - WHO Pain Ladder
1029
+ - Multimodal Analgesia Best Practices
1030
+
1031
+ ## Timeline Generation
1032
+
1033
+ Use the timeline generator script to create visual treatment timelines:
1034
+
1035
+ ```bash
1036
+ python timeline_generator.py --plan my_treatment_plan.tex --output timeline.pdf
1037
+ ```
1038
+
1039
+ Generates:
1040
+ - Gantt chart of treatment phases
1041
+ - Milestone markers for goal assessments
1042
+ - Medication titration schedules
1043
+ - Follow-up appointment calendar
1044
+ - Intervention intensity over time
1045
+
1046
+ ## Support and Resources
1047
+
1048
+ ### Template Generation
1049
+
1050
+ Interactive template selection:
1051
+
1052
+ ```bash
1053
+ cd .claude/skills/treatment-plans/scripts
1054
+ python generate_template.py
1055
+
1056
+ # Or specify type directly
1057
+ python generate_template.py --type mental_health --output depression_treatment_plan.tex
1058
+ ```
1059
+
1060
+ ### Validation Workflow
1061
+
1062
+ 1. **Create treatment plan** using appropriate LaTeX template
1063
+ 2. **Check completeness**: `python check_completeness.py plan.tex`
1064
+ 3. **Validate quality**: `python validate_treatment_plan.py plan.tex`
1065
+ 4. **Review checklist**: Compare against `quality_checklist.md`
1066
+ 5. **Generate PDF**: `pdflatex plan.tex`
1067
+ 6. **Review with patient**: Ensure understanding and agreement
1068
+ 7. **Implement and document**: Track progress in clinical notes
1069
+
1070
+ ### Additional Resources
1071
+
1072
+ - Clinical practice guidelines from specialty societies
1073
+ - AHRQ Effective Health Care Program
1074
+ - Cochrane Library for intervention evidence
1075
+ - UpToDate and DynaMed for treatment recommendations
1076
+ - CMS Quality Measures and HEDIS specifications
1077
+
1078
+ ## Professional Document Styling
1079
+
1080
+ ### Overview
1081
+
1082
+ Treatment plans can be enhanced with professional medical document styling using the `medical_treatment_plan.sty` LaTeX package. This custom style transforms plain academic documents into visually appealing, color-coded clinical documents that maintain scientific rigor while improving readability and usability.
1083
+
1084
+ ### Medical Treatment Plan Style Package
1085
+
1086
+ The `medical_treatment_plan.sty` package (located in `assets/medical_treatment_plan.sty`) provides:
1087
+
1088
+ **Professional Color Scheme**
1089
+ - **Primary Blue** (RGB: 0, 102, 153): Headers, section titles, primary accents
1090
+ - **Secondary Blue** (RGB: 102, 178, 204): Light backgrounds, subtle accents
1091
+ - **Accent Blue** (RGB: 0, 153, 204): Hyperlinks, key highlights
1092
+ - **Success Green** (RGB: 0, 153, 76): Goals, positive outcomes
1093
+ - **Warning Red** (RGB: 204, 0, 0): Warnings, critical information
1094
+ - **Dark Gray** (RGB: 64, 64, 64): Body text
1095
+ - **Light Gray** (RGB: 245, 245, 245): Background fills
1096
+
1097
+ **Styled Elements**
1098
+ - Custom colored headers and footers with professional rules
1099
+ - Blue section titles with underlines for clear hierarchy
1100
+ - Enhanced table formatting with colored headers and alternating rows
1101
+ - Optimized list spacing with colored bullets and numbering
1102
+ - Professional page layout with appropriate margins
1103
+
1104
+ ### Custom Information Boxes
1105
+
1106
+ The style package includes five specialized box environments for organizing clinical information:
1107
+
1108
+ #### 1. Info Box (Blue Border, Light Gray Background)
1109
+
1110
+ For general information, clinical assessments, and testing schedules:
1111
+
1112
+ ```latex
1113
+ \begin{infobox}[Title]
1114
+ \textbf{Key Information:}
1115
+ \begin{itemize}
1116
+ \item Clinical assessment details
1117
+ \item Testing schedules
1118
+ \item General guidance
1119
+ \end{itemize}
1120
+ \end{infobox}
1121
+ ```
1122
+
1123
+ **Use cases**: Metabolic status, baseline assessments, monitoring schedules, titration protocols
1124
+
1125
+ #### 2. Warning Box (Red Border, Yellow Background)
1126
+
1127
+ For critical decision points, safety protocols, and alerts:
1128
+
1129
+ ```latex
1130
+ \begin{warningbox}[Alert Title]
1131
+ \textbf{Important Safety Information:}
1132
+ \begin{itemize}
1133
+ \item Critical drug interactions
1134
+ \item Safety monitoring requirements
1135
+ \item Red flag symptoms requiring immediate action
1136
+ \end{itemize}
1137
+ \end{warningbox}
1138
+ ```
1139
+
1140
+ **Use cases**: Medication safety, decision points, contraindications, emergency protocols
1141
+
1142
+ #### 3. Goal Box (Green Border, Green-Tinted Background)
1143
+
1144
+ For treatment goals, targets, and success criteria:
1145
+
1146
+ ```latex
1147
+ \begin{goalbox}[Treatment Goals]
1148
+ \textbf{Primary Objectives:}
1149
+ \begin{itemize}
1150
+ \item Reduce HbA1c to <7\% within 3 months
1151
+ \item Achieve 5-7\% weight loss in 12 weeks
1152
+ \item Complete diabetes education program
1153
+ \end{itemize}
1154
+ \end{goalbox}
1155
+ ```
1156
+
1157
+ **Use cases**: SMART goals, target outcomes, success metrics, CGM goals
1158
+
1159
+ #### 4. Key Points Box (Blue Background)
1160
+
1161
+ For executive summaries, key takeaways, and important recommendations:
1162
+
1163
+ ```latex
1164
+ \begin{keybox}[Key Highlights]
1165
+ \textbf{Essential Points:}
1166
+ \begin{itemize}
1167
+ \item Main therapeutic approach
1168
+ \item Critical patient instructions
1169
+ \item Priority interventions
1170
+ \end{itemize}
1171
+ \end{keybox}
1172
+ ```
1173
+
1174
+ **Use cases**: Plan overview, plate method instructions, important dietary guidelines
1175
+
1176
+ #### 5. Emergency Box (Large Red Design)
1177
+
1178
+ For emergency contacts and urgent protocols:
1179
+
1180
+ ```latex
1181
+ \begin{emergencybox}
1182
+ \begin{itemize}
1183
+ \item \textbf{Emergency Services:} 911
1184
+ \item \textbf{Endocrinology Office:} [Phone] (business hours)
1185
+ \item \textbf{After-Hours Hotline:} [Phone] (nights/weekends)
1186
+ \item \textbf{Pharmacy:} [Phone and location]
1187
+ \end{itemize}
1188
+ \end{emergencybox}
1189
+ ```
1190
+
1191
+ **Use cases**: Emergency contacts, critical hotlines, urgent resource information
1192
+
1193
+ #### 6. Patient Info Box (White with Blue Border)
1194
+
1195
+ For patient demographics and baseline information:
1196
+
1197
+ ```latex
1198
+ \begin{patientinfo}
1199
+ \begin{tabular}{ll}
1200
+ \textbf{Age:} & 23 years \\
1201
+ \textbf{Sex:} & Male \\
1202
+ \textbf{Diagnosis:} & Type 2 Diabetes Mellitus \\
1203
+ \textbf{Plan Start Date:} & \today \\
1204
+ \end{tabular}
1205
+ \end{patientinfo}
1206
+ ```
1207
+
1208
+ **Use cases**: Patient information sections, demographic data
1209
+
1210
+ ### Professional Table Formatting
1211
+
1212
+ Enhanced table environment with medical styling:
1213
+
1214
+ ```latex
1215
+ \begin{medtable}{Caption Text}
1216
+ \begin{tabular}{|p{5cm}|p{4cm}|p{4.5cm}|}
1217
+ \hline
1218
+ \tableheadercolor % Blue header with white text
1219
+ \textcolor{white}{\textbf{Column 1}} &
1220
+ \textcolor{white}{\textbf{Column 2}} &
1221
+ \textcolor{white}{\textbf{Column 3}} \\
1222
+ \hline
1223
+ Data row 1 content & Value 1 & Details 1 \\
1224
+ \hline
1225
+ \tablerowcolor % Alternating light gray row
1226
+ Data row 2 content & Value 2 & Details 2 \\
1227
+ \hline
1228
+ Data row 3 content & Value 3 & Details 3 \\
1229
+ \hline
1230
+ \end{tabular}
1231
+ \caption{Table caption}
1232
+ \end{medtable}
1233
+ ```
1234
+
1235
+ **Features:**
1236
+ - Blue headers with white text for visual prominence
1237
+ - Alternating row colors (`\tablerowcolor`) for improved readability
1238
+ - Automatic centering and spacing
1239
+ - Professional borders and padding
1240
+
1241
+ ### Using the Style Package
1242
+
1243
+ #### Basic Setup
1244
+
1245
+ 1. **Add to document preamble:**
1246
+
1247
+ ```latex
1248
+ % !TEX program = xelatex
1249
+ \documentclass[11pt,letterpaper]{article}
1250
+
1251
+ % Use custom medical treatment plan style
1252
+ \usepackage{medical_treatment_plan}
1253
+ \usepackage{natbib}
1254
+
1255
+ \begin{document}
1256
+ \maketitle
1257
+ % Your content here
1258
+ \end{document}
1259
+ ```
1260
+
1261
+ 2. **Ensure style file is in same directory** as your `.tex` file, or install to LaTeX path
1262
+
1263
+ 3. **Compile with XeLaTeX** (recommended for best results):
1264
+
1265
+ ```bash
1266
+ xelatex treatment_plan.tex
1267
+ bibtex treatment_plan
1268
+ xelatex treatment_plan.tex
1269
+ xelatex treatment_plan.tex
1270
+ ```
1271
+
1272
+ #### Custom Title Page
1273
+
1274
+ The package automatically formats the title with a professional blue header:
1275
+
1276
+ ```latex
1277
+ \title{\textbf{Individualized Diabetes Treatment Plan}\\
1278
+ \large{23-Year-Old Male Patient with Type 2 Diabetes}}
1279
+ \author{Comprehensive Care Plan}
1280
+ \date{\today}
1281
+
1282
+ \begin{document}
1283
+ \maketitle
1284
+ ```
1285
+
1286
+ This creates an eye-catching blue box with white text and clear hierarchy.
1287
+
1288
+ ### Compilation Requirements
1289
+
1290
+ **Required LaTeX Packages** (automatically loaded by the style):
1291
+ - `geometry` - Page layout and margins
1292
+ - `xcolor` - Color support
1293
+ - `tcolorbox` with `[most]` library - Custom colored boxes
1294
+ - `tikz` - Graphics and drawing
1295
+ - `fontspec` - Font management (XeLaTeX/LuaLaTeX)
1296
+ - `fancyhdr` - Custom headers and footers
1297
+ - `titlesec` - Section styling
1298
+ - `enumitem` - Enhanced list formatting
1299
+ - `booktabs` - Professional table rules
1300
+ - `longtable` - Multi-page tables
1301
+ - `array` - Enhanced table features
1302
+ - `colortbl` - Colored table cells
1303
+ - `hyperref` - Hyperlinks and PDF metadata
1304
+ - `natbib` - Bibliography management
1305
+
1306
+ **Recommended Compilation:**
1307
+
1308
+ ```bash
1309
+ # Using XeLaTeX (best font support)
1310
+ xelatex document.tex
1311
+ bibtex document
1312
+ xelatex document.tex
1313
+ xelatex document.tex
1314
+
1315
+ # Using PDFLaTeX (alternative)
1316
+ pdflatex document.tex
1317
+ bibtex document
1318
+ pdflatex document.tex
1319
+ pdflatex document.tex
1320
+ ```
1321
+
1322
+ ### Customization Options
1323
+
1324
+ #### Changing Colors
1325
+
1326
+ Edit the style file to modify the color scheme:
1327
+
1328
+ ```latex
1329
+ % In medical_treatment_plan.sty
1330
+ \definecolor{primaryblue}{RGB}{0, 102, 153} % Modify these
1331
+ \definecolor{secondaryblue}{RGB}{102, 178, 204}
1332
+ \definecolor{accentblue}{RGB}{0, 153, 204}
1333
+ \definecolor{successgreen}{RGB}{0, 153, 76}
1334
+ \definecolor{warningred}{RGB}{204, 0, 0}
1335
+ ```
1336
+
1337
+ #### Adjusting Page Layout
1338
+
1339
+ Modify geometry settings in the style file:
1340
+
1341
+ ```latex
1342
+ \RequirePackage[margin=1in, top=1.2in, bottom=1.2in]{geometry}
1343
+ ```
1344
+
1345
+ #### Custom Fonts (XeLaTeX only)
1346
+
1347
+ Uncomment and modify in the style file:
1348
+
1349
+ ```latex
1350
+ \setmainfont{Your Preferred Font}
1351
+ \setsansfont{Your Sans-Serif Font}
1352
+ ```
1353
+
1354
+ #### Header/Footer Customization
1355
+
1356
+ Modify in the style file:
1357
+
1358
+ ```latex
1359
+ \fancyhead[L]{\color{primaryblue}\sffamily\small\textbf{Treatment Plan Title}}
1360
+ \fancyhead[R]{\color{darkgray}\sffamily\small Patient Info}
1361
+ ```
1362
+
1363
+ ### Style Package Download and Installation
1364
+
1365
+ #### Option 1: Copy to Project Directory
1366
+
1367
+ Copy `assets/medical_treatment_plan.sty` to the same directory as your `.tex` file.
1368
+
1369
+ #### Option 2: Install to User TeX Directory
1370
+
1371
+ ```bash
1372
+ # Find your local texmf directory
1373
+ kpsewhich -var-value TEXMFHOME
1374
+
1375
+ # Copy to appropriate location (usually ~/texmf/tex/latex/)
1376
+ mkdir -p ~/texmf/tex/latex/medical_treatment_plan
1377
+ cp assets/medical_treatment_plan.sty ~/texmf/tex/latex/medical_treatment_plan/
1378
+
1379
+ # Update TeX file database
1380
+ texhash ~/texmf
1381
+ ```
1382
+
1383
+ #### Option 3: System-Wide Installation
1384
+
1385
+ ```bash
1386
+ # Copy to system texmf directory (requires sudo)
1387
+ sudo cp assets/medical_treatment_plan.sty /usr/local/texlive/texmf-local/tex/latex/
1388
+ sudo texhash
1389
+ ```
1390
+
1391
+ ### Additional Professional Styles (Optional)
1392
+
1393
+ Other medical/clinical document styles available from CTAN:
1394
+
1395
+ **Journal Styles:**
1396
+ ```bash
1397
+ # Install via TeX Live Manager
1398
+ tlmgr install nejm # New England Journal of Medicine
1399
+ tlmgr install jama # JAMA style
1400
+ tlmgr install bmj # British Medical Journal
1401
+ ```
1402
+
1403
+ **General Professional Styles:**
1404
+ ```bash
1405
+ tlmgr install apa7 # APA 7th edition (health sciences)
1406
+ tlmgr install IEEEtran # IEEE (medical devices/engineering)
1407
+ tlmgr install springer # Springer journals
1408
+ ```
1409
+
1410
+ **Download from CTAN:**
1411
+ - Visit: https://ctan.org/
1412
+ - Search for medical document classes
1413
+ - Download and install per package instructions
1414
+
1415
+ ### Troubleshooting
1416
+
1417
+ **Issue: Package not found**
1418
+ ```bash
1419
+ # Install missing packages via TeX Live Manager
1420
+ sudo tlmgr update --self
1421
+ sudo tlmgr install tcolorbox tikz pgf
1422
+ ```
1423
+
1424
+ **Issue: Missing characters (✓, ≥, etc.)**
1425
+ - Use XeLaTeX instead of PDFLaTeX
1426
+ - Or replace with LaTeX commands: `$\checkmark$`, `$\geq$`
1427
+ - Requires `amssymb` package for math symbols
1428
+
1429
+ **Issue: Header height warnings**
1430
+ - Style file sets `\setlength{\headheight}{22pt}`
1431
+ - Adjust if needed for your content
1432
+
1433
+ **Issue: Boxes not rendering**
1434
+ ```bash
1435
+ # Ensure complete tcolorbox installation
1436
+ sudo tlmgr install tcolorbox tikz pgf
1437
+ ```
1438
+
1439
+ **Issue: Font not found (XeLaTeX)**
1440
+ - Comment out custom font lines in .sty file
1441
+ - Or install specified fonts on your system
1442
+
1443
+ ### Best Practices for Styled Documents
1444
+
1445
+ 1. **Appropriate Box Usage**
1446
+ - Match box type to content purpose (goals→green, warnings→yellow/red)
1447
+ - Don't overuse boxes; reserve for truly important information
1448
+ - Keep box content concise and focused
1449
+
1450
+ 2. **Visual Hierarchy**
1451
+ - Use section styling for structure
1452
+ - Boxes for emphasis and organization
1453
+ - Tables for comparative data
1454
+ - Lists for sequential or grouped items
1455
+
1456
+ 3. **Color Consistency**
1457
+ - Stick to defined color scheme
1458
+ - Use `\textcolor{primaryblue}{\textbf{Text}}` for emphasis
1459
+ - Maintain consistent meaning (red=warning, green=goals)
1460
+
1461
+ 4. **White Space**
1462
+ - Don't overcrowd pages with boxes
1463
+ - Use `\vspace{0.5cm}` between major sections
1464
+ - Allow breathing room around colored elements
1465
+
1466
+ 5. **Professional Appearance**
1467
+ - Maintain readability as top priority
1468
+ - Ensure sufficient contrast for accessibility
1469
+ - Test print output in grayscale
1470
+ - Keep styling consistent throughout document
1471
+
1472
+ 6. **Table Formatting**
1473
+ - Use `\tableheadercolor` for all header rows
1474
+ - Apply `\tablerowcolor` to alternating rows in tables >3 rows
1475
+ - Keep column widths balanced
1476
+ - Use `\small\sffamily` for large tables
1477
+
1478
+ ### Example: Styled Treatment Plan Structure
1479
+
1480
+ ```latex
1481
+ % !TEX program = xelatex
1482
+ \documentclass[11pt,letterpaper]{article}
1483
+ \usepackage{medical_treatment_plan}
1484
+ \usepackage{natbib}
1485
+
1486
+ \title{\textbf{Comprehensive Treatment Plan}\\
1487
+ \large{Patient-Centered Care Strategy}}
1488
+ \author{Multidisciplinary Care Team}
1489
+ \date{\today}
1490
+
1491
+ \begin{document}
1492
+ \maketitle
1493
+
1494
+ \section*{Patient Information}
1495
+ \begin{patientinfo}
1496
+ % Demographics table
1497
+ \end{patientinfo}
1498
+
1499
+ \section{Executive Summary}
1500
+ \begin{keybox}[Plan Overview]
1501
+ % Key highlights
1502
+ \end{keybox}
1503
+
1504
+ \section{Treatment Goals}
1505
+ \begin{goalbox}[SMART Goals - 3 Months]
1506
+ \begin{medtable}{Primary Treatment Targets}
1507
+ % Goals table with colored headers
1508
+ \end{medtable}
1509
+ \end{goalbox}
1510
+
1511
+ \section{Medication Plan}
1512
+ \begin{infobox}[Titration Schedule]
1513
+ % Medication instructions
1514
+ \end{infobox}
1515
+
1516
+ \begin{warningbox}[Critical Decision Point]
1517
+ % Important safety information
1518
+ \end{warningbox}
1519
+
1520
+ \section{Emergency Protocols}
1521
+ \begin{emergencybox}
1522
+ % Emergency contacts
1523
+ \end{emergencybox}
1524
+
1525
+ \bibliographystyle{plainnat}
1526
+ \bibliography{references}
1527
+ \end{document}
1528
+ ```
1529
+
1530
+ ### Benefits of Professional Styling
1531
+
1532
+ **Clinical Practice:**
1533
+ - Faster information scanning during patient encounters
1534
+ - Clear visual hierarchy for critical vs. routine information
1535
+ - Professional appearance suitable for patient-facing documents
1536
+ - Color-coded sections reduce cognitive load
1537
+
1538
+ **Educational Use:**
1539
+ - Enhanced readability for teaching materials
1540
+ - Visual differentiation of concept types (goals, warnings, procedures)
1541
+ - Professional presentation for case discussions
1542
+ - Print and digital-ready formats
1543
+
1544
+ **Documentation Quality:**
1545
+ - Modern, polished appearance
1546
+ - Maintains clinical accuracy while improving aesthetics
1547
+ - Standardized formatting across treatment plans
1548
+ - Easy to customize for institutional branding
1549
+
1550
+ **Patient Engagement:**
1551
+ - More approachable than dense text documents
1552
+ - Color coding helps patients identify key sections
1553
+ - Professional appearance builds trust
1554
+ - Clear organization facilitates understanding
1555
+
1556
+ ## Ethical Considerations
1557
+
1558
+ ### Informed Consent
1559
+ All treatment plans should involve patient understanding and voluntary agreement to proposed interventions.
1560
+
1561
+ ### Cultural Sensitivity
1562
+ Treatment plans must respect diverse cultural beliefs, health practices, and communication styles.
1563
+
1564
+ ### Health Equity
1565
+ Consider social determinants of health, access barriers, and health disparities when developing plans.
1566
+
1567
+ ### Privacy Protection
1568
+ Maintain strict HIPAA compliance; de-identify all protected health information in shared documents.
1569
+
1570
+ ### Autonomy and Beneficence
1571
+ Balance medical recommendations with patient autonomy and values while promoting patient welfare.
1572
+
1573
+ ## License
1574
+
1575
+ Part of the Claude Scientific Writer project. See main LICENSE file.
1576
+