@bgicli/bgicli 2.1.1 → 2.2.0

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 (1266) hide show
  1. package/data/skills/aav-vector-design-agent/SKILL.md +198 -0
  2. package/data/skills/adaptyv/SKILL.md +112 -0
  3. package/data/skills/adhd-daily-planner/SKILL.md +271 -0
  4. package/data/skills/aeon/SKILL.md +372 -0
  5. package/data/skills/agent-browser/SKILL.md +159 -0
  6. package/data/skills/agentd-drug-discovery/SKILL.md +52 -0
  7. package/data/skills/ai-analyzer/SKILL.md +218 -0
  8. package/data/skills/alphafold/SKILL.md +183 -0
  9. package/data/skills/alphafold-database/SKILL.md +500 -0
  10. package/data/skills/anndata/SKILL.md +394 -0
  11. package/data/skills/antibody-design-agent/SKILL.md +64 -0
  12. package/data/skills/arboreto/SKILL.md +237 -0
  13. package/data/skills/armored-cart-design-agent/SKILL.md +225 -0
  14. package/data/skills/arxiv-search/SKILL.md +224 -0
  15. package/data/skills/autonomous-oncology-agent/SKILL.md +77 -0
  16. package/data/skills/bayesian-optimizer/SKILL.md +60 -0
  17. package/data/skills/benchling-integration/SKILL.md +473 -0
  18. package/data/skills/bgpt-paper-search/SKILL.md +81 -0
  19. package/data/skills/bindcraft/SKILL.md +198 -0
  20. package/data/skills/binder-design/SKILL.md +182 -0
  21. package/data/skills/binding-characterization/SKILL.md +234 -0
  22. package/data/skills/bindingdb-database/SKILL.md +332 -0
  23. package/data/skills/bio-admet-prediction/SKILL.md +224 -0
  24. package/data/skills/bio-alignment-files-bam-statistics/SKILL.md +340 -0
  25. package/data/skills/bio-alignment-filtering/SKILL.md +322 -0
  26. package/data/skills/bio-alignment-indexing/SKILL.md +249 -0
  27. package/data/skills/bio-alignment-io/SKILL.md +301 -0
  28. package/data/skills/bio-alignment-msa-parsing/SKILL.md +366 -0
  29. package/data/skills/bio-alignment-msa-statistics/SKILL.md +375 -0
  30. package/data/skills/bio-alignment-pairwise/SKILL.md +277 -0
  31. package/data/skills/bio-alignment-sorting/SKILL.md +296 -0
  32. package/data/skills/bio-alignment-validation/SKILL.md +374 -0
  33. package/data/skills/bio-atac-seq-atac-peak-calling/SKILL.md +221 -0
  34. package/data/skills/bio-atac-seq-atac-qc/SKILL.md +292 -0
  35. package/data/skills/bio-atac-seq-differential-accessibility/SKILL.md +268 -0
  36. package/data/skills/bio-atac-seq-footprinting/SKILL.md +256 -0
  37. package/data/skills/bio-atac-seq-motif-deviation/SKILL.md +319 -0
  38. package/data/skills/bio-atac-seq-nucleosome-positioning/SKILL.md +321 -0
  39. package/data/skills/bio-basecalling/SKILL.md +368 -0
  40. package/data/skills/bio-batch-downloads/SKILL.md +384 -0
  41. package/data/skills/bio-batch-processing/SKILL.md +303 -0
  42. package/data/skills/bio-bedgraph-handling/SKILL.md +336 -0
  43. package/data/skills/bio-blast-searches/SKILL.md +354 -0
  44. package/data/skills/bio-causal-genomics-colocalization-analysis/SKILL.md +264 -0
  45. package/data/skills/bio-causal-genomics-fine-mapping/SKILL.md +267 -0
  46. package/data/skills/bio-causal-genomics-mediation-analysis/SKILL.md +264 -0
  47. package/data/skills/bio-causal-genomics-mendelian-randomization/SKILL.md +221 -0
  48. package/data/skills/bio-causal-genomics-pleiotropy-detection/SKILL.md +292 -0
  49. package/data/skills/bio-cfdna-preprocessing/SKILL.md +200 -0
  50. package/data/skills/bio-chipseq-differential-binding/SKILL.md +262 -0
  51. package/data/skills/bio-chipseq-motif-analysis/SKILL.md +387 -0
  52. package/data/skills/bio-chipseq-peak-annotation/SKILL.md +239 -0
  53. package/data/skills/bio-chipseq-peak-calling/SKILL.md +277 -0
  54. package/data/skills/bio-chipseq-qc/SKILL.md +391 -0
  55. package/data/skills/bio-chipseq-super-enhancers/SKILL.md +288 -0
  56. package/data/skills/bio-chipseq-visualization/SKILL.md +289 -0
  57. package/data/skills/bio-clinical-databases-clinvar-lookup/SKILL.md +188 -0
  58. package/data/skills/bio-clinical-databases-dbsnp-queries/SKILL.md +171 -0
  59. package/data/skills/bio-clinical-databases-gnomad-frequencies/SKILL.md +205 -0
  60. package/data/skills/bio-clinical-databases-hla-typing/SKILL.md +248 -0
  61. package/data/skills/bio-clinical-databases-myvariant-queries/SKILL.md +174 -0
  62. package/data/skills/bio-clinical-databases-pharmacogenomics/SKILL.md +232 -0
  63. package/data/skills/bio-clinical-databases-polygenic-risk/SKILL.md +276 -0
  64. package/data/skills/bio-clinical-databases-somatic-signatures/SKILL.md +261 -0
  65. package/data/skills/bio-clinical-databases-tumor-mutational-burden/SKILL.md +301 -0
  66. package/data/skills/bio-clinical-databases-variant-prioritization/SKILL.md +225 -0
  67. package/data/skills/bio-clip-seq-binding-site-annotation/SKILL.md +66 -0
  68. package/data/skills/bio-clip-seq-clip-alignment/SKILL.md +70 -0
  69. package/data/skills/bio-clip-seq-clip-motif-analysis/SKILL.md +62 -0
  70. package/data/skills/bio-clip-seq-clip-peak-calling/SKILL.md +282 -0
  71. package/data/skills/bio-clip-seq-clip-preprocessing/SKILL.md +142 -0
  72. package/data/skills/bio-codon-usage/SKILL.md +353 -0
  73. package/data/skills/bio-comparative-genomics-ancestral-reconstruction/SKILL.md +312 -0
  74. package/data/skills/bio-comparative-genomics-hgt-detection/SKILL.md +341 -0
  75. package/data/skills/bio-comparative-genomics-ortholog-inference/SKILL.md +308 -0
  76. package/data/skills/bio-comparative-genomics-positive-selection/SKILL.md +354 -0
  77. package/data/skills/bio-comparative-genomics-synteny-analysis/SKILL.md +315 -0
  78. package/data/skills/bio-compressed-files/SKILL.md +263 -0
  79. package/data/skills/bio-consensus-sequences/SKILL.md +340 -0
  80. package/data/skills/bio-copy-number-cnv-annotation/SKILL.md +307 -0
  81. package/data/skills/bio-copy-number-cnv-visualization/SKILL.md +294 -0
  82. package/data/skills/bio-copy-number-cnvkit-analysis/SKILL.md +290 -0
  83. package/data/skills/bio-copy-number-gatk-cnv/SKILL.md +270 -0
  84. package/data/skills/bio-crispr-screens-base-editing-analysis/SKILL.md +110 -0
  85. package/data/skills/bio-crispr-screens-batch-correction/SKILL.md +316 -0
  86. package/data/skills/bio-crispr-screens-crispresso-editing/SKILL.md +205 -0
  87. package/data/skills/bio-crispr-screens-hit-calling/SKILL.md +264 -0
  88. package/data/skills/bio-crispr-screens-jacks-analysis/SKILL.md +313 -0
  89. package/data/skills/bio-crispr-screens-library-design/SKILL.md +417 -0
  90. package/data/skills/bio-crispr-screens-mageck-analysis/SKILL.md +222 -0
  91. package/data/skills/bio-crispr-screens-screen-qc/SKILL.md +243 -0
  92. package/data/skills/bio-ctdna-mutation-detection/SKILL.md +234 -0
  93. package/data/skills/bio-data-visualization-circos-plots/SKILL.md +405 -0
  94. package/data/skills/bio-data-visualization-color-palettes/SKILL.md +244 -0
  95. package/data/skills/bio-data-visualization-genome-browser-tracks/SKILL.md +328 -0
  96. package/data/skills/bio-data-visualization-genome-tracks/SKILL.md +249 -0
  97. package/data/skills/bio-data-visualization-ggplot2-fundamentals/SKILL.md +313 -0
  98. package/data/skills/bio-data-visualization-heatmaps-clustering/SKILL.md +227 -0
  99. package/data/skills/bio-data-visualization-interactive-visualization/SKILL.md +210 -0
  100. package/data/skills/bio-data-visualization-multipanel-figures/SKILL.md +274 -0
  101. package/data/skills/bio-data-visualization-specialized-omics-plots/SKILL.md +251 -0
  102. package/data/skills/bio-data-visualization-upset-plots/SKILL.md +228 -0
  103. package/data/skills/bio-data-visualization-volcano-customization/SKILL.md +233 -0
  104. package/data/skills/bio-de-deseq2-basics/SKILL.md +376 -0
  105. package/data/skills/bio-de-edger-basics/SKILL.md +418 -0
  106. package/data/skills/bio-de-results/SKILL.md +378 -0
  107. package/data/skills/bio-de-visualization/SKILL.md +408 -0
  108. package/data/skills/bio-differential-expression-batch-correction/SKILL.md +253 -0
  109. package/data/skills/bio-differential-expression-timeseries-de/SKILL.md +370 -0
  110. package/data/skills/bio-differential-splicing/SKILL.md +177 -0
  111. package/data/skills/bio-duplicate-handling/SKILL.md +292 -0
  112. package/data/skills/bio-entrez-fetch/SKILL.md +334 -0
  113. package/data/skills/bio-entrez-link/SKILL.md +325 -0
  114. package/data/skills/bio-entrez-search/SKILL.md +311 -0
  115. package/data/skills/bio-epidemiological-genomics-amr-surveillance/SKILL.md +233 -0
  116. package/data/skills/bio-epidemiological-genomics-pathogen-typing/SKILL.md +202 -0
  117. package/data/skills/bio-epidemiological-genomics-phylodynamics/SKILL.md +207 -0
  118. package/data/skills/bio-epidemiological-genomics-transmission-inference/SKILL.md +237 -0
  119. package/data/skills/bio-epidemiological-genomics-variant-surveillance/SKILL.md +237 -0
  120. package/data/skills/bio-epitranscriptomics-m6a-differential/SKILL.md +88 -0
  121. package/data/skills/bio-epitranscriptomics-m6a-peak-calling/SKILL.md +89 -0
  122. package/data/skills/bio-epitranscriptomics-m6anet-analysis/SKILL.md +101 -0
  123. package/data/skills/bio-epitranscriptomics-merip-preprocessing/SKILL.md +81 -0
  124. package/data/skills/bio-epitranscriptomics-modification-visualization/SKILL.md +98 -0
  125. package/data/skills/bio-experimental-design-batch-design/SKILL.md +110 -0
  126. package/data/skills/bio-experimental-design-multiple-testing/SKILL.md +98 -0
  127. package/data/skills/bio-experimental-design-power-analysis/SKILL.md +84 -0
  128. package/data/skills/bio-experimental-design-sample-size/SKILL.md +93 -0
  129. package/data/skills/bio-expression-matrix-counts-ingest/SKILL.md +220 -0
  130. package/data/skills/bio-expression-matrix-gene-id-mapping/SKILL.md +256 -0
  131. package/data/skills/bio-expression-matrix-metadata-joins/SKILL.md +271 -0
  132. package/data/skills/bio-expression-matrix-sparse-handling/SKILL.md +247 -0
  133. package/data/skills/bio-fastq-quality/SKILL.md +279 -0
  134. package/data/skills/bio-filter-sequences/SKILL.md +265 -0
  135. package/data/skills/bio-flow-cytometry-bead-normalization/SKILL.md +315 -0
  136. package/data/skills/bio-flow-cytometry-clustering-phenotyping/SKILL.md +237 -0
  137. package/data/skills/bio-flow-cytometry-compensation-transformation/SKILL.md +196 -0
  138. package/data/skills/bio-flow-cytometry-cytometry-qc/SKILL.md +382 -0
  139. package/data/skills/bio-flow-cytometry-differential-analysis/SKILL.md +217 -0
  140. package/data/skills/bio-flow-cytometry-doublet-detection/SKILL.md +288 -0
  141. package/data/skills/bio-flow-cytometry-fcs-handling/SKILL.md +221 -0
  142. package/data/skills/bio-flow-cytometry-gating-analysis/SKILL.md +193 -0
  143. package/data/skills/bio-format-conversion/SKILL.md +193 -0
  144. package/data/skills/bio-fragment-analysis/SKILL.md +214 -0
  145. package/data/skills/bio-gatk-variant-calling/SKILL.md +422 -0
  146. package/data/skills/bio-genome-assembly-assembly-polishing/SKILL.md +333 -0
  147. package/data/skills/bio-genome-assembly-assembly-qc/SKILL.md +344 -0
  148. package/data/skills/bio-genome-assembly-contamination-detection/SKILL.md +235 -0
  149. package/data/skills/bio-genome-assembly-hifi-assembly/SKILL.md +178 -0
  150. package/data/skills/bio-genome-assembly-long-read-assembly/SKILL.md +307 -0
  151. package/data/skills/bio-genome-assembly-metagenome-assembly/SKILL.md +227 -0
  152. package/data/skills/bio-genome-assembly-scaffolding/SKILL.md +204 -0
  153. package/data/skills/bio-genome-assembly-short-read-assembly/SKILL.md +319 -0
  154. package/data/skills/bio-genome-engineering-base-editing-design/SKILL.md +277 -0
  155. package/data/skills/bio-genome-engineering-grna-design/SKILL.md +221 -0
  156. package/data/skills/bio-genome-engineering-hdr-template-design/SKILL.md +264 -0
  157. package/data/skills/bio-genome-engineering-off-target-prediction/SKILL.md +232 -0
  158. package/data/skills/bio-genome-engineering-prime-editing-design/SKILL.md +275 -0
  159. package/data/skills/bio-genome-intervals-bed-file-basics/SKILL.md +357 -0
  160. package/data/skills/bio-genome-intervals-bigwig-tracks/SKILL.md +351 -0
  161. package/data/skills/bio-genome-intervals-coverage-analysis/SKILL.md +300 -0
  162. package/data/skills/bio-genome-intervals-gtf-gff-handling/SKILL.md +345 -0
  163. package/data/skills/bio-genome-intervals-interval-arithmetic/SKILL.md +485 -0
  164. package/data/skills/bio-genome-intervals-proximity-operations/SKILL.md +337 -0
  165. package/data/skills/bio-geo-data/SKILL.md +380 -0
  166. package/data/skills/bio-hi-c-analysis-compartment-analysis/SKILL.md +261 -0
  167. package/data/skills/bio-hi-c-analysis-contact-pairs/SKILL.md +278 -0
  168. package/data/skills/bio-hi-c-analysis-hic-data-io/SKILL.md +260 -0
  169. package/data/skills/bio-hi-c-analysis-hic-differential/SKILL.md +328 -0
  170. package/data/skills/bio-hi-c-analysis-hic-visualization/SKILL.md +297 -0
  171. package/data/skills/bio-hi-c-analysis-loop-calling/SKILL.md +284 -0
  172. package/data/skills/bio-hi-c-analysis-matrix-operations/SKILL.md +274 -0
  173. package/data/skills/bio-hi-c-analysis-tad-detection/SKILL.md +239 -0
  174. package/data/skills/bio-imaging-mass-cytometry-cell-segmentation/SKILL.md +241 -0
  175. package/data/skills/bio-imaging-mass-cytometry-data-preprocessing/SKILL.md +279 -0
  176. package/data/skills/bio-imaging-mass-cytometry-interactive-annotation/SKILL.md +304 -0
  177. package/data/skills/bio-imaging-mass-cytometry-phenotyping/SKILL.md +231 -0
  178. package/data/skills/bio-imaging-mass-cytometry-quality-metrics/SKILL.md +316 -0
  179. package/data/skills/bio-imaging-mass-cytometry-spatial-analysis/SKILL.md +246 -0
  180. package/data/skills/bio-immunoinformatics-epitope-prediction/SKILL.md +259 -0
  181. package/data/skills/bio-immunoinformatics-immunogenicity-scoring/SKILL.md +275 -0
  182. package/data/skills/bio-immunoinformatics-mhc-binding-prediction/SKILL.md +260 -0
  183. package/data/skills/bio-immunoinformatics-neoantigen-prediction/SKILL.md +277 -0
  184. package/data/skills/bio-immunoinformatics-tcr-epitope-binding/SKILL.md +257 -0
  185. package/data/skills/bio-isoform-switching/SKILL.md +192 -0
  186. package/data/skills/bio-liquid-biopsy-pipeline/SKILL.md +311 -0
  187. package/data/skills/bio-local-blast/SKILL.md +350 -0
  188. package/data/skills/bio-long-read-sequencing-clair3-variants/SKILL.md +252 -0
  189. package/data/skills/bio-long-read-sequencing-isoseq-analysis/SKILL.md +334 -0
  190. package/data/skills/bio-long-read-sequencing-nanopore-methylation/SKILL.md +110 -0
  191. package/data/skills/bio-longitudinal-monitoring/SKILL.md +271 -0
  192. package/data/skills/bio-longread-alignment/SKILL.md +193 -0
  193. package/data/skills/bio-longread-medaka/SKILL.md +176 -0
  194. package/data/skills/bio-longread-qc/SKILL.md +224 -0
  195. package/data/skills/bio-longread-structural-variants/SKILL.md +201 -0
  196. package/data/skills/bio-machine-learning-atlas-mapping/SKILL.md +139 -0
  197. package/data/skills/bio-machine-learning-biomarker-discovery/SKILL.md +157 -0
  198. package/data/skills/bio-machine-learning-model-validation/SKILL.md +148 -0
  199. package/data/skills/bio-machine-learning-omics-classifiers/SKILL.md +146 -0
  200. package/data/skills/bio-machine-learning-prediction-explanation/SKILL.md +162 -0
  201. package/data/skills/bio-machine-learning-survival-analysis/SKILL.md +176 -0
  202. package/data/skills/bio-metabolomics-lipidomics/SKILL.md +265 -0
  203. package/data/skills/bio-metabolomics-metabolite-annotation/SKILL.md +241 -0
  204. package/data/skills/bio-metabolomics-msdial-preprocessing/SKILL.md +308 -0
  205. package/data/skills/bio-metabolomics-normalization-qc/SKILL.md +283 -0
  206. package/data/skills/bio-metabolomics-pathway-mapping/SKILL.md +237 -0
  207. package/data/skills/bio-metabolomics-statistical-analysis/SKILL.md +276 -0
  208. package/data/skills/bio-metabolomics-targeted-analysis/SKILL.md +314 -0
  209. package/data/skills/bio-metabolomics-xcms-preprocessing/SKILL.md +268 -0
  210. package/data/skills/bio-metagenomics-abundance/SKILL.md +203 -0
  211. package/data/skills/bio-metagenomics-amr-detection/SKILL.md +293 -0
  212. package/data/skills/bio-metagenomics-functional-profiling/SKILL.md +252 -0
  213. package/data/skills/bio-metagenomics-kraken/SKILL.md +204 -0
  214. package/data/skills/bio-metagenomics-metaphlan/SKILL.md +214 -0
  215. package/data/skills/bio-metagenomics-strain-tracking/SKILL.md +292 -0
  216. package/data/skills/bio-metagenomics-visualization/SKILL.md +240 -0
  217. package/data/skills/bio-methylation-based-detection/SKILL.md +223 -0
  218. package/data/skills/bio-methylation-bismark-alignment/SKILL.md +195 -0
  219. package/data/skills/bio-methylation-calling/SKILL.md +200 -0
  220. package/data/skills/bio-methylation-dmr-detection/SKILL.md +211 -0
  221. package/data/skills/bio-methylation-methylkit/SKILL.md +219 -0
  222. package/data/skills/bio-microbiome-amplicon-processing/SKILL.md +137 -0
  223. package/data/skills/bio-microbiome-differential-abundance/SKILL.md +147 -0
  224. package/data/skills/bio-microbiome-diversity-analysis/SKILL.md +188 -0
  225. package/data/skills/bio-microbiome-functional-prediction/SKILL.md +153 -0
  226. package/data/skills/bio-microbiome-qiime2-workflow/SKILL.md +219 -0
  227. package/data/skills/bio-microbiome-taxonomy-assignment/SKILL.md +168 -0
  228. package/data/skills/bio-molecular-descriptors/SKILL.md +200 -0
  229. package/data/skills/bio-molecular-io/SKILL.md +188 -0
  230. package/data/skills/bio-motif-search/SKILL.md +354 -0
  231. package/data/skills/bio-multi-omics-data-harmonization/SKILL.md +228 -0
  232. package/data/skills/bio-multi-omics-mixomics-analysis/SKILL.md +221 -0
  233. package/data/skills/bio-multi-omics-mofa-integration/SKILL.md +225 -0
  234. package/data/skills/bio-multi-omics-similarity-network/SKILL.md +235 -0
  235. package/data/skills/bio-orchestrator/SKILL.md +133 -0
  236. package/data/skills/bio-paired-end-fastq/SKILL.md +334 -0
  237. package/data/skills/bio-pathway-enrichment-visualization/SKILL.md +278 -0
  238. package/data/skills/bio-pathway-go-enrichment/SKILL.md +218 -0
  239. package/data/skills/bio-pathway-gsea/SKILL.md +227 -0
  240. package/data/skills/bio-pathway-kegg-pathways/SKILL.md +234 -0
  241. package/data/skills/bio-pathway-reactome/SKILL.md +215 -0
  242. package/data/skills/bio-pathway-wikipathways/SKILL.md +255 -0
  243. package/data/skills/bio-pdb-geometric-analysis/SKILL.md +475 -0
  244. package/data/skills/bio-pdb-structure-io/SKILL.md +296 -0
  245. package/data/skills/bio-pdb-structure-modification/SKILL.md +448 -0
  246. package/data/skills/bio-pdb-structure-navigation/SKILL.md +335 -0
  247. package/data/skills/bio-phasing-imputation-genotype-imputation/SKILL.md +201 -0
  248. package/data/skills/bio-phasing-imputation-haplotype-phasing/SKILL.md +190 -0
  249. package/data/skills/bio-phasing-imputation-imputation-qc/SKILL.md +265 -0
  250. package/data/skills/bio-phasing-imputation-reference-panels/SKILL.md +203 -0
  251. package/data/skills/bio-phylo-distance-calculations/SKILL.md +307 -0
  252. package/data/skills/bio-phylo-modern-tree-inference/SKILL.md +274 -0
  253. package/data/skills/bio-phylo-tree-io/SKILL.md +252 -0
  254. package/data/skills/bio-phylo-tree-manipulation/SKILL.md +375 -0
  255. package/data/skills/bio-phylo-tree-visualization/SKILL.md +275 -0
  256. package/data/skills/bio-pileup-generation/SKILL.md +314 -0
  257. package/data/skills/bio-population-genetics-association-testing/SKILL.md +293 -0
  258. package/data/skills/bio-population-genetics-linkage-disequilibrium/SKILL.md +260 -0
  259. package/data/skills/bio-population-genetics-plink-basics/SKILL.md +338 -0
  260. package/data/skills/bio-population-genetics-population-structure/SKILL.md +352 -0
  261. package/data/skills/bio-population-genetics-scikit-allel-analysis/SKILL.md +306 -0
  262. package/data/skills/bio-population-genetics-selection-statistics/SKILL.md +251 -0
  263. package/data/skills/bio-primer-design-primer-basics/SKILL.md +289 -0
  264. package/data/skills/bio-primer-design-primer-validation/SKILL.md +344 -0
  265. package/data/skills/bio-primer-design-qpcr-primers/SKILL.md +273 -0
  266. package/data/skills/bio-proteomics-data-import/SKILL.md +122 -0
  267. package/data/skills/bio-proteomics-dia-analysis/SKILL.md +246 -0
  268. package/data/skills/bio-proteomics-differential-abundance/SKILL.md +129 -0
  269. package/data/skills/bio-proteomics-peptide-identification/SKILL.md +122 -0
  270. package/data/skills/bio-proteomics-protein-inference/SKILL.md +174 -0
  271. package/data/skills/bio-proteomics-proteomics-qc/SKILL.md +208 -0
  272. package/data/skills/bio-proteomics-ptm-analysis/SKILL.md +139 -0
  273. package/data/skills/bio-proteomics-quantification/SKILL.md +141 -0
  274. package/data/skills/bio-proteomics-spectral-libraries/SKILL.md +270 -0
  275. package/data/skills/bio-reaction-enumeration/SKILL.md +251 -0
  276. package/data/skills/bio-read-alignment-bowtie2-alignment/SKILL.md +189 -0
  277. package/data/skills/bio-read-alignment-bwa-alignment/SKILL.md +166 -0
  278. package/data/skills/bio-read-alignment-hisat2-alignment/SKILL.md +205 -0
  279. package/data/skills/bio-read-alignment-star-alignment/SKILL.md +204 -0
  280. package/data/skills/bio-read-qc-adapter-trimming/SKILL.md +222 -0
  281. package/data/skills/bio-read-qc-contamination-screening/SKILL.md +252 -0
  282. package/data/skills/bio-read-qc-fastp-workflow/SKILL.md +278 -0
  283. package/data/skills/bio-read-qc-quality-filtering/SKILL.md +231 -0
  284. package/data/skills/bio-read-qc-quality-reports/SKILL.md +204 -0
  285. package/data/skills/bio-read-qc-umi-processing/SKILL.md +391 -0
  286. package/data/skills/bio-read-sequences/SKILL.md +319 -0
  287. package/data/skills/bio-reference-operations/SKILL.md +302 -0
  288. package/data/skills/bio-reporting-automated-qc-reports/SKILL.md +103 -0
  289. package/data/skills/bio-reporting-figure-export/SKILL.md +112 -0
  290. package/data/skills/bio-reporting-jupyter-reports/SKILL.md +98 -0
  291. package/data/skills/bio-reporting-quarto-reports/SKILL.md +295 -0
  292. package/data/skills/bio-reporting-rmarkdown-reports/SKILL.md +276 -0
  293. package/data/skills/bio-research-tools-biomarker-signature-studio/SKILL.md +99 -0
  294. package/data/skills/bio-restriction-enzyme-selection/SKILL.md +342 -0
  295. package/data/skills/bio-restriction-fragment-analysis/SKILL.md +259 -0
  296. package/data/skills/bio-restriction-mapping/SKILL.md +239 -0
  297. package/data/skills/bio-restriction-sites/SKILL.md +222 -0
  298. package/data/skills/bio-reverse-complement/SKILL.md +250 -0
  299. package/data/skills/bio-ribo-seq-orf-detection/SKILL.md +303 -0
  300. package/data/skills/bio-ribo-seq-riboseq-preprocessing/SKILL.md +176 -0
  301. package/data/skills/bio-ribo-seq-ribosome-periodicity/SKILL.md +182 -0
  302. package/data/skills/bio-ribo-seq-ribosome-stalling/SKILL.md +217 -0
  303. package/data/skills/bio-ribo-seq-translation-efficiency/SKILL.md +183 -0
  304. package/data/skills/bio-rna-quantification-alignment-free-quant/SKILL.md +226 -0
  305. package/data/skills/bio-rna-quantification-count-matrix-qc/SKILL.md +310 -0
  306. package/data/skills/bio-rna-quantification-featurecounts-counting/SKILL.md +190 -0
  307. package/data/skills/bio-rna-quantification-tximport-workflow/SKILL.md +240 -0
  308. package/data/skills/bio-rnaseq-qc/SKILL.md +320 -0
  309. package/data/skills/bio-sam-bam-basics/SKILL.md +248 -0
  310. package/data/skills/bio-sashimi-plots/SKILL.md +175 -0
  311. package/data/skills/bio-seq-objects/SKILL.md +240 -0
  312. package/data/skills/bio-sequence-properties/SKILL.md +397 -0
  313. package/data/skills/bio-sequence-similarity/SKILL.md +335 -0
  314. package/data/skills/bio-sequence-slicing/SKILL.md +232 -0
  315. package/data/skills/bio-sequence-statistics/SKILL.md +318 -0
  316. package/data/skills/bio-similarity-searching/SKILL.md +200 -0
  317. package/data/skills/bio-single-cell-batch-integration/SKILL.md +317 -0
  318. package/data/skills/bio-single-cell-cell-annotation/SKILL.md +259 -0
  319. package/data/skills/bio-single-cell-cell-communication/SKILL.md +257 -0
  320. package/data/skills/bio-single-cell-clustering/SKILL.md +330 -0
  321. package/data/skills/bio-single-cell-data-io/SKILL.md +315 -0
  322. package/data/skills/bio-single-cell-doublet-detection/SKILL.md +362 -0
  323. package/data/skills/bio-single-cell-lineage-tracing/SKILL.md +319 -0
  324. package/data/skills/bio-single-cell-markers-annotation/SKILL.md +317 -0
  325. package/data/skills/bio-single-cell-metabolite-communication/SKILL.md +258 -0
  326. package/data/skills/bio-single-cell-multimodal-integration/SKILL.md +242 -0
  327. package/data/skills/bio-single-cell-perturb-seq/SKILL.md +258 -0
  328. package/data/skills/bio-single-cell-preprocessing/SKILL.md +338 -0
  329. package/data/skills/bio-single-cell-scatac-analysis/SKILL.md +326 -0
  330. package/data/skills/bio-single-cell-splicing/SKILL.md +199 -0
  331. package/data/skills/bio-single-cell-trajectory-inference/SKILL.md +225 -0
  332. package/data/skills/bio-small-rna-seq-differential-mirna/SKILL.md +194 -0
  333. package/data/skills/bio-small-rna-seq-mirdeep2-analysis/SKILL.md +180 -0
  334. package/data/skills/bio-small-rna-seq-mirge3-analysis/SKILL.md +178 -0
  335. package/data/skills/bio-small-rna-seq-smrna-preprocessing/SKILL.md +174 -0
  336. package/data/skills/bio-small-rna-seq-target-prediction/SKILL.md +202 -0
  337. package/data/skills/bio-spatial-transcriptomics-image-analysis/SKILL.md +283 -0
  338. package/data/skills/bio-spatial-transcriptomics-spatial-communication/SKILL.md +299 -0
  339. package/data/skills/bio-spatial-transcriptomics-spatial-data-io/SKILL.md +272 -0
  340. package/data/skills/bio-spatial-transcriptomics-spatial-deconvolution/SKILL.md +314 -0
  341. package/data/skills/bio-spatial-transcriptomics-spatial-domains/SKILL.md +254 -0
  342. package/data/skills/bio-spatial-transcriptomics-spatial-multiomics/SKILL.md +181 -0
  343. package/data/skills/bio-spatial-transcriptomics-spatial-neighbors/SKILL.md +198 -0
  344. package/data/skills/bio-spatial-transcriptomics-spatial-preprocessing/SKILL.md +269 -0
  345. package/data/skills/bio-spatial-transcriptomics-spatial-proteomics/SKILL.md +124 -0
  346. package/data/skills/bio-spatial-transcriptomics-spatial-statistics/SKILL.md +237 -0
  347. package/data/skills/bio-spatial-transcriptomics-spatial-visualization/SKILL.md +287 -0
  348. package/data/skills/bio-splicing-pipeline/SKILL.md +253 -0
  349. package/data/skills/bio-splicing-qc/SKILL.md +190 -0
  350. package/data/skills/bio-splicing-quantification/SKILL.md +145 -0
  351. package/data/skills/bio-sra-data/SKILL.md +363 -0
  352. package/data/skills/bio-structural-biology-alphafold-predictions/SKILL.md +258 -0
  353. package/data/skills/bio-structural-biology-modern-structure-prediction/SKILL.md +346 -0
  354. package/data/skills/bio-substructure-search/SKILL.md +206 -0
  355. package/data/skills/bio-systems-biology-context-specific-models/SKILL.md +241 -0
  356. package/data/skills/bio-systems-biology-flux-balance-analysis/SKILL.md +206 -0
  357. package/data/skills/bio-systems-biology-gene-essentiality/SKILL.md +235 -0
  358. package/data/skills/bio-systems-biology-metabolic-reconstruction/SKILL.md +215 -0
  359. package/data/skills/bio-systems-biology-model-curation/SKILL.md +243 -0
  360. package/data/skills/bio-tcr-bcr-analysis-immcantation-analysis/SKILL.md +195 -0
  361. package/data/skills/bio-tcr-bcr-analysis-mixcr-analysis/SKILL.md +167 -0
  362. package/data/skills/bio-tcr-bcr-analysis-repertoire-visualization/SKILL.md +224 -0
  363. package/data/skills/bio-tcr-bcr-analysis-scirpy-analysis/SKILL.md +168 -0
  364. package/data/skills/bio-tcr-bcr-analysis-vdjtools-analysis/SKILL.md +188 -0
  365. package/data/skills/bio-transcription-translation/SKILL.md +237 -0
  366. package/data/skills/bio-tumor-fraction-estimation/SKILL.md +211 -0
  367. package/data/skills/bio-uniprot-access/SKILL.md +239 -0
  368. package/data/skills/bio-variant-annotation/SKILL.md +410 -0
  369. package/data/skills/bio-variant-calling/SKILL.md +266 -0
  370. package/data/skills/bio-variant-calling-clinical-interpretation/SKILL.md +355 -0
  371. package/data/skills/bio-variant-calling-deepvariant/SKILL.md +315 -0
  372. package/data/skills/bio-variant-calling-filtering-best-practices/SKILL.md +403 -0
  373. package/data/skills/bio-variant-calling-joint-calling/SKILL.md +338 -0
  374. package/data/skills/bio-variant-calling-structural-variant-calling/SKILL.md +253 -0
  375. package/data/skills/bio-variant-normalization/SKILL.md +325 -0
  376. package/data/skills/bio-vcf-basics/SKILL.md +342 -0
  377. package/data/skills/bio-vcf-manipulation/SKILL.md +429 -0
  378. package/data/skills/bio-vcf-statistics/SKILL.md +445 -0
  379. package/data/skills/bio-virtual-screening/SKILL.md +263 -0
  380. package/data/skills/bio-workflow-management-cwl-workflows/SKILL.md +433 -0
  381. package/data/skills/bio-workflow-management-nextflow-pipelines/SKILL.md +386 -0
  382. package/data/skills/bio-workflow-management-snakemake-workflows/SKILL.md +383 -0
  383. package/data/skills/bio-workflow-management-wdl-workflows/SKILL.md +500 -0
  384. package/data/skills/bio-workflows-atacseq-pipeline/SKILL.md +362 -0
  385. package/data/skills/bio-workflows-biomarker-pipeline/SKILL.md +272 -0
  386. package/data/skills/bio-workflows-chipseq-pipeline/SKILL.md +282 -0
  387. package/data/skills/bio-workflows-clip-pipeline/SKILL.md +268 -0
  388. package/data/skills/bio-workflows-cnv-pipeline/SKILL.md +324 -0
  389. package/data/skills/bio-workflows-crispr-editing-pipeline/SKILL.md +455 -0
  390. package/data/skills/bio-workflows-crispr-screen-pipeline/SKILL.md +278 -0
  391. package/data/skills/bio-workflows-cytometry-pipeline/SKILL.md +328 -0
  392. package/data/skills/bio-workflows-expression-to-pathways/SKILL.md +329 -0
  393. package/data/skills/bio-workflows-fastq-to-variants/SKILL.md +374 -0
  394. package/data/skills/bio-workflows-genome-assembly-pipeline/SKILL.md +290 -0
  395. package/data/skills/bio-workflows-gwas-pipeline/SKILL.md +323 -0
  396. package/data/skills/bio-workflows-hic-pipeline/SKILL.md +304 -0
  397. package/data/skills/bio-workflows-imc-pipeline/SKILL.md +304 -0
  398. package/data/skills/bio-workflows-longread-sv-pipeline/SKILL.md +281 -0
  399. package/data/skills/bio-workflows-merip-pipeline/SKILL.md +222 -0
  400. package/data/skills/bio-workflows-metabolic-modeling-pipeline/SKILL.md +408 -0
  401. package/data/skills/bio-workflows-metabolomics-pipeline/SKILL.md +297 -0
  402. package/data/skills/bio-workflows-metagenomics-pipeline/SKILL.md +283 -0
  403. package/data/skills/bio-workflows-methylation-pipeline/SKILL.md +274 -0
  404. package/data/skills/bio-workflows-microbiome-pipeline/SKILL.md +221 -0
  405. package/data/skills/bio-workflows-multi-omics-pipeline/SKILL.md +362 -0
  406. package/data/skills/bio-workflows-multiome-pipeline/SKILL.md +298 -0
  407. package/data/skills/bio-workflows-neoantigen-pipeline/SKILL.md +325 -0
  408. package/data/skills/bio-workflows-outbreak-pipeline/SKILL.md +341 -0
  409. package/data/skills/bio-workflows-proteomics-pipeline/SKILL.md +226 -0
  410. package/data/skills/bio-workflows-riboseq-pipeline/SKILL.md +94 -0
  411. package/data/skills/bio-workflows-rnaseq-to-de/SKILL.md +345 -0
  412. package/data/skills/bio-workflows-scrnaseq-pipeline/SKILL.md +354 -0
  413. package/data/skills/bio-workflows-smrna-pipeline/SKILL.md +86 -0
  414. package/data/skills/bio-workflows-somatic-variant-pipeline/SKILL.md +313 -0
  415. package/data/skills/bio-workflows-spatial-pipeline/SKILL.md +267 -0
  416. package/data/skills/bio-workflows-tcr-pipeline/SKILL.md +84 -0
  417. package/data/skills/bio-write-sequences/SKILL.md +205 -0
  418. package/data/skills/bioinformatics-singlecell/SKILL.md +143 -0
  419. package/data/skills/biokernel/SKILL.md +61 -0
  420. package/data/skills/biologist-analyst/SKILL.md +799 -0
  421. package/data/skills/biomaster-workflows/SKILL.md +55 -0
  422. package/data/skills/biomcp-server/SKILL.md +65 -0
  423. package/data/skills/biomedical-data-analysis/SKILL.md +56 -0
  424. package/data/skills/biomedical-search/SKILL.md +214 -0
  425. package/data/skills/biomni/SKILL.md +309 -0
  426. package/data/skills/biomni-general-agent/SKILL.md +43 -0
  427. package/data/skills/biomni-research-agent/SKILL.md +76 -0
  428. package/data/skills/biopython/SKILL.md +437 -0
  429. package/data/skills/biorxiv-database/SKILL.md +477 -0
  430. package/data/skills/bioservices/SKILL.md +355 -0
  431. package/data/skills/boltz/SKILL.md +188 -0
  432. package/data/skills/boltzgen/SKILL.md +287 -0
  433. package/data/skills/bone-marrow-ai-agent/SKILL.md +163 -0
  434. package/data/skills/brainstorming/SKILL.md +96 -0
  435. package/data/skills/brenda-database/SKILL.md +714 -0
  436. package/data/skills/bulk-combat-correction/SKILL.md +54 -0
  437. package/data/skills/bulk-deg-analysis/SKILL.md +61 -0
  438. package/data/skills/bulk-deseq2-analysis/SKILL.md +50 -0
  439. package/data/skills/bulk-stringdb-ppi/SKILL.md +49 -0
  440. package/data/skills/bulk-to-single-deconvolution/SKILL.md +50 -0
  441. package/data/skills/bulk-trajblend-interpolation/SKILL.md +52 -0
  442. package/data/skills/bulk-wgcna-analysis/SKILL.md +56 -0
  443. package/data/skills/cancer-metabolism-agent/SKILL.md +180 -0
  444. package/data/skills/care-coordination/SKILL.md +35 -0
  445. package/data/skills/cart-design-optimizer-agent/SKILL.md +162 -0
  446. package/data/skills/cbioportal-database/SKILL.md +367 -0
  447. package/data/skills/cell-free-expression/SKILL.md +291 -0
  448. package/data/skills/cellagent-annotation/SKILL.md +69 -0
  449. package/data/skills/cellfree-rna-agent/SKILL.md +182 -0
  450. package/data/skills/cellular-senescence-agent/SKILL.md +183 -0
  451. package/data/skills/cellxgene-census/SKILL.md +505 -0
  452. package/data/skills/chai/SKILL.md +272 -0
  453. package/data/skills/chatehr-clinician-assistant/SKILL.md +67 -0
  454. package/data/skills/chematagent-drug-discovery/SKILL.md +68 -0
  455. package/data/skills/chembl-database/SKILL.md +383 -0
  456. package/data/skills/chembl-search/SKILL.md +211 -0
  457. package/data/skills/chemcrow-drug-discovery/SKILL.md +61 -0
  458. package/data/skills/chemical-property-lookup/SKILL.md +42 -0
  459. package/data/skills/chemist-analyst/SKILL.md +1603 -0
  460. package/data/skills/chemistry-agent/SKILL.md +62 -0
  461. package/data/skills/chip-clonal-hematopoiesis-agent/SKILL.md +224 -0
  462. package/data/skills/chromosomal-instability-agent/SKILL.md +187 -0
  463. package/data/skills/citation-management/SKILL.md +1081 -0
  464. package/data/skills/claims-appeals/SKILL.md +35 -0
  465. package/data/skills/claw-ancestry-pca/SKILL.md +145 -0
  466. package/data/skills/claw-metagenomics/SKILL.md +238 -0
  467. package/data/skills/claw-semantic-sim/SKILL.md +151 -0
  468. package/data/skills/clinical-decision-support/SKILL.md +504 -0
  469. package/data/skills/clinical-diagnostic-reasoning/SKILL.md +222 -0
  470. package/data/skills/clinical-nlp-extractor/SKILL.md +59 -0
  471. package/data/skills/clinical-note-summarization/SKILL.md +52 -0
  472. package/data/skills/clinical-reports/SKILL.md +1127 -0
  473. package/data/skills/clinical-trial-protocol-skill/SKILL.md +508 -0
  474. package/data/skills/clinical-trials-search/SKILL.md +211 -0
  475. package/data/skills/clinicaltrials-database/SKILL.md +501 -0
  476. package/data/skills/clinpgx/SKILL.md +96 -0
  477. package/data/skills/clinpgx-database/SKILL.md +632 -0
  478. package/data/skills/clinvar-database/SKILL.md +356 -0
  479. package/data/skills/cnv-caller-agent/SKILL.md +171 -0
  480. package/data/skills/coagulation-thrombosis-agent/SKILL.md +141 -0
  481. package/data/skills/cobrapy/SKILL.md +457 -0
  482. package/data/skills/compbioagent-explorer/SKILL.md +67 -0
  483. package/data/skills/computational-pathology-agent/SKILL.md +72 -0
  484. package/data/skills/convergence-study/SKILL.md +98 -0
  485. package/data/skills/cosmic-database/SKILL.md +330 -0
  486. package/data/skills/crisis-detection-intervention-ai/SKILL.md +569 -0
  487. package/data/skills/crisis-response-protocol/SKILL.md +456 -0
  488. package/data/skills/crispr-guide-design/SKILL.md +72 -0
  489. package/data/skills/crispr-offtarget-predictor/SKILL.md +56 -0
  490. package/data/skills/cryoem-ai-drug-design-agent/SKILL.md +216 -0
  491. package/data/skills/ctdna-dynamics-mrd-agent/SKILL.md +206 -0
  492. package/data/skills/cytokine-storm-analysis-agent/SKILL.md +180 -0
  493. package/data/skills/dask/SKILL.md +454 -0
  494. package/data/skills/data-stats-analysis/SKILL.md +477 -0
  495. package/data/skills/data-transform/SKILL.md +576 -0
  496. package/data/skills/data-visualization-biomedical/SKILL.md +252 -0
  497. package/data/skills/data-visualization-expert/SKILL.md +72 -0
  498. package/data/skills/data-viz-plots/SKILL.md +461 -0
  499. package/data/skills/datacommons-client/SKILL.md +253 -0
  500. package/data/skills/datamol/SKILL.md +700 -0
  501. package/data/skills/deep-research/SKILL.md +111 -0
  502. package/data/skills/deep-research-swarm/SKILL.md +62 -0
  503. package/data/skills/deep-visual-proteomics-agent/SKILL.md +149 -0
  504. package/data/skills/deepchem/SKILL.md +591 -0
  505. package/data/skills/deeptools/SKILL.md +525 -0
  506. package/data/skills/depmap/SKILL.md +300 -0
  507. package/data/skills/diffdock/SKILL.md +477 -0
  508. package/data/skills/differentiation-schemes/SKILL.md +159 -0
  509. package/data/skills/digital-twin-clinical-agent/SKILL.md +228 -0
  510. package/data/skills/dispatching-parallel-agents/SKILL.md +180 -0
  511. package/data/skills/dnanexus-integration/SKILL.md +376 -0
  512. package/data/skills/doc-coauthoring/SKILL.md +375 -0
  513. package/data/skills/docx/SKILL.md +590 -0
  514. package/data/skills/docx-official/SKILL.md +197 -0
  515. package/data/skills/drug-discovery-search/SKILL.md +214 -0
  516. package/data/skills/drug-interaction-checker/SKILL.md +56 -0
  517. package/data/skills/drug-labels-search/SKILL.md +211 -0
  518. package/data/skills/drug-photo/SKILL.md +149 -0
  519. package/data/skills/drugbank-database/SKILL.md +184 -0
  520. package/data/skills/drugbank-search/SKILL.md +211 -0
  521. package/data/skills/ehr-fhir-integration/SKILL.md +60 -0
  522. package/data/skills/emergency-card/SKILL.md +426 -0
  523. package/data/skills/ena-database/SKILL.md +198 -0
  524. package/data/skills/ensembl-database/SKILL.md +305 -0
  525. package/data/skills/epidemiologist-analyst/SKILL.md +1844 -0
  526. package/data/skills/epigenomics-methylgpt-agent/SKILL.md +111 -0
  527. package/data/skills/equity-scorer/SKILL.md +182 -0
  528. package/data/skills/esm/SKILL.md +300 -0
  529. package/data/skills/etetoolkit/SKILL.md +617 -0
  530. package/data/skills/executing-plans/SKILL.md +84 -0
  531. package/data/skills/exosome-ev-analysis-agent/SKILL.md +171 -0
  532. package/data/skills/exploratory-data-analysis/SKILL.md +440 -0
  533. package/data/skills/family-health-analyzer/SKILL.md +137 -0
  534. package/data/skills/fastq-analysis/SKILL.md +191 -0
  535. package/data/skills/fda-database/SKILL.md +512 -0
  536. package/data/skills/fhir-developer-skill/SKILL.md +294 -0
  537. package/data/skills/fhir-development/SKILL.md +35 -0
  538. package/data/skills/find-skills/SKILL.md +133 -0
  539. package/data/skills/finishing-a-development-branch/SKILL.md +200 -0
  540. package/data/skills/fitness-analyzer/SKILL.md +431 -0
  541. package/data/skills/flowio/SKILL.md +602 -0
  542. package/data/skills/foldseek/SKILL.md +179 -0
  543. package/data/skills/galaxy-bridge/SKILL.md +215 -0
  544. package/data/skills/gene-database/SKILL.md +173 -0
  545. package/data/skills/gene-panel-design-agent/SKILL.md +192 -0
  546. package/data/skills/geniml/SKILL.md +312 -0
  547. package/data/skills/genome-compare/SKILL.md +127 -0
  548. package/data/skills/geo-database/SKILL.md +809 -0
  549. package/data/skills/geopandas/SKILL.md +245 -0
  550. package/data/skills/gget/SKILL.md +865 -0
  551. package/data/skills/ginkgo-cloud-lab/SKILL.md +56 -0
  552. package/data/skills/glycoengineering/SKILL.md +338 -0
  553. package/data/skills/gnomad-database/SKILL.md +395 -0
  554. package/data/skills/goal-analyzer/SKILL.md +605 -0
  555. package/data/skills/grief-companion/SKILL.md +250 -0
  556. package/data/skills/gsea-enrichment/SKILL.md +151 -0
  557. package/data/skills/gtars/SKILL.md +279 -0
  558. package/data/skills/gtex-database/SKILL.md +315 -0
  559. package/data/skills/gwas-database/SKILL.md +602 -0
  560. package/data/skills/gwas-lookup/SKILL.md +122 -0
  561. package/data/skills/gwas-prs/SKILL.md +178 -0
  562. package/data/skills/health-trend-analyzer/SKILL.md +451 -0
  563. package/data/skills/hemoglobinopathy-analysis-agent/SKILL.md +167 -0
  564. package/data/skills/hipaa-compliance/SKILL.md +230 -0
  565. package/data/skills/histolab/SKILL.md +672 -0
  566. package/data/skills/hmdb-database/SKILL.md +190 -0
  567. package/data/skills/hrd-analysis-agent/SKILL.md +184 -0
  568. package/data/skills/hrv-alexithymia-expert/SKILL.md +151 -0
  569. package/data/skills/hypogenic/SKILL.md +649 -0
  570. package/data/skills/hypothesis-generation/SKILL.md +286 -0
  571. package/data/skills/imaging-data-commons/SKILL.md +843 -0
  572. package/data/skills/immune-checkpoint-combination-agent/SKILL.md +170 -0
  573. package/data/skills/infographics/SKILL.md +563 -0
  574. package/data/skills/instrument-data-to-allotrope/SKILL.md +280 -0
  575. package/data/skills/interpro-database/SKILL.md +305 -0
  576. package/data/skills/ipsae/SKILL.md +190 -0
  577. package/data/skills/iso-13485-certification/SKILL.md +678 -0
  578. package/data/skills/jaspar-database/SKILL.md +351 -0
  579. package/data/skills/jungian-psychologist/SKILL.md +191 -0
  580. package/data/skills/kegg-database/SKILL.md +371 -0
  581. package/data/skills/knowledge-synthesis/SKILL.md +283 -0
  582. package/data/skills/kragen-knowledge-graph/SKILL.md +68 -0
  583. package/data/skills/lab-results/SKILL.md +35 -0
  584. package/data/skills/labarchive-integration/SKILL.md +262 -0
  585. package/data/skills/labstep/SKILL.md +208 -0
  586. package/data/skills/lamindb/SKILL.md +384 -0
  587. package/data/skills/latchbio-integration/SKILL.md +347 -0
  588. package/data/skills/latex-posters/SKILL.md +1602 -0
  589. package/data/skills/leads-literature-mining/SKILL.md +68 -0
  590. package/data/skills/ligandmpnn/SKILL.md +170 -0
  591. package/data/skills/linear-solvers/SKILL.md +165 -0
  592. package/data/skills/liquid-biopsy-analytics-agent/SKILL.md +171 -0
  593. package/data/skills/lit-synthesizer/SKILL.md +53 -0
  594. package/data/skills/literature-review/SKILL.md +584 -0
  595. package/data/skills/literature-search/SKILL.md +214 -0
  596. package/data/skills/lobster-bioinformatics/SKILL.md +305 -0
  597. package/data/skills/long-read-sequencing-agent/SKILL.md +181 -0
  598. package/data/skills/mage-antibody-generator/SKILL.md +54 -0
  599. package/data/skills/markdown-mermaid-writing/SKILL.md +327 -0
  600. package/data/skills/markitdown/SKILL.md +486 -0
  601. package/data/skills/matchms/SKILL.md +197 -0
  602. package/data/skills/matplotlib/SKILL.md +359 -0
  603. package/data/skills/mcpmed-bioinformatics-server/SKILL.md +42 -0
  604. package/data/skills/medchem/SKILL.md +400 -0
  605. package/data/skills/medea-therapeutic-discovery/SKILL.md +45 -0
  606. package/data/skills/medical-entity-extractor/SKILL.md +144 -0
  607. package/data/skills/medical-imaging-review/SKILL.md +170 -0
  608. package/data/skills/medical-research-toolkit/SKILL.md +273 -0
  609. package/data/skills/medrxiv-search/SKILL.md +211 -0
  610. package/data/skills/mental-health-analyzer/SKILL.md +981 -0
  611. package/data/skills/mesh-generation/SKILL.md +149 -0
  612. package/data/skills/metabolomics-workbench-database/SKILL.md +253 -0
  613. package/data/skills/microbiome-cancer-agent/SKILL.md +180 -0
  614. package/data/skills/modern-drug-rehab-computer/SKILL.md +392 -0
  615. package/data/skills/molecular-dynamics/SKILL.md +457 -0
  616. package/data/skills/molecular-glue-discovery-agent/SKILL.md +224 -0
  617. package/data/skills/molecule-evolution-agent/SKILL.md +62 -0
  618. package/data/skills/molfeat/SKILL.md +505 -0
  619. package/data/skills/monarch-database/SKILL.md +372 -0
  620. package/data/skills/mpn-progression-monitor-agent/SKILL.md +228 -0
  621. package/data/skills/mpn-research-assistant/SKILL.md +197 -0
  622. package/data/skills/mrd-edge-detection-agent/SKILL.md +213 -0
  623. package/data/skills/multi-ancestry-prs-agent/SKILL.md +224 -0
  624. package/data/skills/multi-search-engine/SKILL.md +110 -0
  625. package/data/skills/multimodal-medical-imaging/SKILL.md +59 -0
  626. package/data/skills/multimodal-radpath-fusion-agent/SKILL.md +213 -0
  627. package/data/skills/myeloma-mrd-agent/SKILL.md +184 -0
  628. package/data/skills/networkx/SKILL.md +435 -0
  629. package/data/skills/neurokit2/SKILL.md +350 -0
  630. package/data/skills/neuropixels-analysis/SKILL.md +344 -0
  631. package/data/skills/nextflow-development/SKILL.md +290 -0
  632. package/data/skills/ngs-analysis/SKILL.md +183 -0
  633. package/data/skills/nicheformer-spatial-agent/SKILL.md +197 -0
  634. package/data/skills/nk-cell-therapy-agent/SKILL.md +186 -0
  635. package/data/skills/nonlinear-solvers/SKILL.md +180 -0
  636. package/data/skills/numerical-integration/SKILL.md +166 -0
  637. package/data/skills/numerical-stability/SKILL.md +149 -0
  638. package/data/skills/nutrition-analyzer/SKILL.md +775 -0
  639. package/data/skills/occupational-health-analyzer/SKILL.md +386 -0
  640. package/data/skills/omero-integration/SKILL.md +245 -0
  641. package/data/skills/ontology-explorer/SKILL.md +168 -0
  642. package/data/skills/ontology-mapper/SKILL.md +171 -0
  643. package/data/skills/ontology-validator/SKILL.md +136 -0
  644. package/data/skills/open-notebook/SKILL.md +289 -0
  645. package/data/skills/open-targets-search/SKILL.md +211 -0
  646. package/data/skills/openalex-database/SKILL.md +488 -0
  647. package/data/skills/opentargets-database/SKILL.md +367 -0
  648. package/data/skills/opentrons-integration/SKILL.md +567 -0
  649. package/data/skills/opentrons-protocol-agent/SKILL.md +58 -0
  650. package/data/skills/organoid-drug-response-agent/SKILL.md +189 -0
  651. package/data/skills/pan-cancer-multiomics-agent/SKILL.md +159 -0
  652. package/data/skills/paper-2-web/SKILL.md +495 -0
  653. package/data/skills/parameter-optimization/SKILL.md +141 -0
  654. package/data/skills/patents-search/SKILL.md +211 -0
  655. package/data/skills/pathml/SKILL.md +160 -0
  656. package/data/skills/patiently-ai/SKILL.md +103 -0
  657. package/data/skills/pdb/SKILL.md +217 -0
  658. package/data/skills/pdb-database/SKILL.md +303 -0
  659. package/data/skills/pdf/SKILL.md +314 -0
  660. package/data/skills/pdf-anthropic/SKILL.md +294 -0
  661. package/data/skills/pdf-processing/SKILL.md +149 -0
  662. package/data/skills/pdf-processing-pro/SKILL.md +296 -0
  663. package/data/skills/pdx-model-analysis-agent/SKILL.md +169 -0
  664. package/data/skills/peer-review/SKILL.md +565 -0
  665. package/data/skills/performance-profiling/SKILL.md +255 -0
  666. package/data/skills/perplexity-search/SKILL.md +441 -0
  667. package/data/skills/pharmacogenomics-agent/SKILL.md +143 -0
  668. package/data/skills/pharmgx-reporter/SKILL.md +134 -0
  669. package/data/skills/phylogenetics/SKILL.md +404 -0
  670. package/data/skills/plotly/SKILL.md +265 -0
  671. package/data/skills/polars/SKILL.md +385 -0
  672. package/data/skills/popeve-variant-predictor-agent/SKILL.md +213 -0
  673. package/data/skills/post-processing/SKILL.md +338 -0
  674. package/data/skills/pptx/SKILL.md +232 -0
  675. package/data/skills/pptx-official/SKILL.md +484 -0
  676. package/data/skills/pptx-posters/SKILL.md +414 -0
  677. package/data/skills/precision-oncology-agent/SKILL.md +53 -0
  678. package/data/skills/prior-auth-coworker/SKILL.md +60 -0
  679. package/data/skills/prior-auth-review-skill/SKILL.md +360 -0
  680. package/data/skills/profile-report/SKILL.md +120 -0
  681. package/data/skills/protac-design-agent/SKILL.md +220 -0
  682. package/data/skills/protein-design-workflow/SKILL.md +199 -0
  683. package/data/skills/protein-qc/SKILL.md +300 -0
  684. package/data/skills/protein-structure-prediction/SKILL.md +59 -0
  685. package/data/skills/proteinmpnn/SKILL.md +279 -0
  686. package/data/skills/protocolsio-integration/SKILL.md +415 -0
  687. package/data/skills/prs-net-deep-learning-agent/SKILL.md +232 -0
  688. package/data/skills/psychologist-analyst/SKILL.md +1888 -0
  689. package/data/skills/pubchem-database/SKILL.md +568 -0
  690. package/data/skills/pubmed-database/SKILL.md +454 -0
  691. package/data/skills/pubmed-search/SKILL.md +103 -0
  692. package/data/skills/pydeseq2/SKILL.md +553 -0
  693. package/data/skills/pydicom/SKILL.md +428 -0
  694. package/data/skills/pyhealth/SKILL.md +485 -0
  695. package/data/skills/pylabrobot/SKILL.md +179 -0
  696. package/data/skills/pymc/SKILL.md +566 -0
  697. package/data/skills/pymoo/SKILL.md +565 -0
  698. package/data/skills/pyopenms/SKILL.md +211 -0
  699. package/data/skills/pysam/SKILL.md +259 -0
  700. package/data/skills/pytdc/SKILL.md +454 -0
  701. package/data/skills/pytorch-lightning/SKILL.md +172 -0
  702. package/data/skills/pyzotero/SKILL.md +111 -0
  703. package/data/skills/radgpt-radiology-reporter/SKILL.md +67 -0
  704. package/data/skills/radiomics-pathomics-fusion-agent/SKILL.md +221 -0
  705. package/data/skills/rdkit/SKILL.md +763 -0
  706. package/data/skills/reactome-database/SKILL.md +272 -0
  707. package/data/skills/receiving-code-review/SKILL.md +213 -0
  708. package/data/skills/recovery-community-moderator/SKILL.md +175 -0
  709. package/data/skills/regulatory-drafter/SKILL.md +56 -0
  710. package/data/skills/regulatory-drafting/SKILL.md +35 -0
  711. package/data/skills/rehabilitation-analyzer/SKILL.md +636 -0
  712. package/data/skills/repro-enforcer/SKILL.md +50 -0
  713. package/data/skills/requesting-code-review/SKILL.md +105 -0
  714. package/data/skills/research-grants/SKILL.md +935 -0
  715. package/data/skills/research-literature/SKILL.md +35 -0
  716. package/data/skills/research-lookup/SKILL.md +502 -0
  717. package/data/skills/rfdiffusion/SKILL.md +306 -0
  718. package/data/skills/rna-velocity-agent/SKILL.md +174 -0
  719. package/data/skills/scanpy/SKILL.md +380 -0
  720. package/data/skills/scfoundation-model-agent/SKILL.md +210 -0
  721. package/data/skills/scientific-brainstorming/SKILL.md +185 -0
  722. package/data/skills/scientific-critical-thinking/SKILL.md +566 -0
  723. package/data/skills/scientific-manuscript/SKILL.md +181 -0
  724. package/data/skills/scientific-problem-selection/SKILL.md +269 -0
  725. package/data/skills/scientific-schematics/SKILL.md +619 -0
  726. package/data/skills/scientific-slides/SKILL.md +1154 -0
  727. package/data/skills/scientific-visualization/SKILL.md +773 -0
  728. package/data/skills/scientific-writing/SKILL.md +483 -0
  729. package/data/skills/scikit-bio/SKILL.md +431 -0
  730. package/data/skills/scikit-learn/SKILL.md +515 -0
  731. package/data/skills/scikit-survival/SKILL.md +393 -0
  732. package/data/skills/scrna-orchestrator/SKILL.md +204 -0
  733. package/data/skills/scrna-qc/SKILL.md +43 -0
  734. package/data/skills/scvelo/SKILL.md +321 -0
  735. package/data/skills/scvi-tools/SKILL.md +184 -0
  736. package/data/skills/seaborn/SKILL.md +671 -0
  737. package/data/skills/search-strategy/SKILL.md +247 -0
  738. package/data/skills/seq-wrangler/SKILL.md +58 -0
  739. package/data/skills/shap/SKILL.md +560 -0
  740. package/data/skills/simo-multiomics-integration-agent/SKILL.md +178 -0
  741. package/data/skills/simpy/SKILL.md +423 -0
  742. package/data/skills/simulation-orchestrator/SKILL.md +230 -0
  743. package/data/skills/simulation-validator/SKILL.md +195 -0
  744. package/data/skills/single-annotation/SKILL.md +129 -0
  745. package/data/skills/single-cell-rna-qc/SKILL.md +175 -0
  746. package/data/skills/single-cellphone-db/SKILL.md +68 -0
  747. package/data/skills/single-clustering/SKILL.md +75 -0
  748. package/data/skills/single-downstream-analysis/SKILL.md +150 -0
  749. package/data/skills/single-multiomics/SKILL.md +44 -0
  750. package/data/skills/single-preprocessing/SKILL.md +184 -0
  751. package/data/skills/single-to-spatial-mapping/SKILL.md +48 -0
  752. package/data/skills/single-trajectory/SKILL.md +62 -0
  753. package/data/skills/sleep-analyzer/SKILL.md +773 -0
  754. package/data/skills/slurm-job-script-generator/SKILL.md +135 -0
  755. package/data/skills/solublempnn/SKILL.md +165 -0
  756. package/data/skills/spatial-agent/SKILL.md +56 -0
  757. package/data/skills/spatial-epigenomics-agent/SKILL.md +163 -0
  758. package/data/skills/spatial-transcriptomics-agent/SKILL.md +75 -0
  759. package/data/skills/spatial-transcriptomics-analysis/SKILL.md +72 -0
  760. package/data/skills/spatial-transcriptomics-analysis/STAgent/SKILL.md +75 -0
  761. package/data/skills/spatial-transcriptomics-analysis/SpatialAgent/SKILL.md +56 -0
  762. package/data/skills/spatial-transcriptomics-analysis/bioSkills/image-analysis/SKILL.md +266 -0
  763. package/data/skills/spatial-transcriptomics-analysis/bioSkills/spatial-communication/SKILL.md +287 -0
  764. package/data/skills/spatial-transcriptomics-analysis/bioSkills/spatial-data-io/SKILL.md +243 -0
  765. package/data/skills/spatial-transcriptomics-analysis/bioSkills/spatial-deconvolution/SKILL.md +298 -0
  766. package/data/skills/spatial-transcriptomics-analysis/bioSkills/spatial-domains/SKILL.md +229 -0
  767. package/data/skills/spatial-transcriptomics-analysis/bioSkills/spatial-multiomics/SKILL.md +172 -0
  768. package/data/skills/spatial-transcriptomics-analysis/bioSkills/spatial-neighbors/SKILL.md +189 -0
  769. package/data/skills/spatial-transcriptomics-analysis/bioSkills/spatial-preprocessing/SKILL.md +232 -0
  770. package/data/skills/spatial-transcriptomics-analysis/bioSkills/spatial-proteomics/SKILL.md +127 -0
  771. package/data/skills/spatial-transcriptomics-analysis/bioSkills/spatial-statistics/SKILL.md +225 -0
  772. package/data/skills/spatial-transcriptomics-analysis/bioSkills/spatial-visualization/SKILL.md +270 -0
  773. package/data/skills/spatial-tutorials/SKILL.md +87 -0
  774. package/data/skills/speech-pathology-ai/SKILL.md +184 -0
  775. package/data/skills/statistical-analysis/SKILL.md +626 -0
  776. package/data/skills/statsmodels/SKILL.md +608 -0
  777. package/data/skills/string-database/SKILL.md +528 -0
  778. package/data/skills/struct-predictor/SKILL.md +52 -0
  779. package/data/skills/subagent-driven-development/SKILL.md +242 -0
  780. package/data/skills/systematic-debugging/SKILL.md +296 -0
  781. package/data/skills/tcell-exhaustion-analysis-agent/SKILL.md +139 -0
  782. package/data/skills/tcga-preprocessing/SKILL.md +49 -0
  783. package/data/skills/tcm-constitution-analyzer/SKILL.md +664 -0
  784. package/data/skills/tcr-pmhc-prediction-agent/SKILL.md +226 -0
  785. package/data/skills/tcr-repertoire-analysis-agent/SKILL.md +218 -0
  786. package/data/skills/test-driven-development/SKILL.md +371 -0
  787. package/data/skills/tiledbvcf/SKILL.md +459 -0
  788. package/data/skills/time-resolved-cryoem-agent/SKILL.md +223 -0
  789. package/data/skills/time-stepping/SKILL.md +140 -0
  790. package/data/skills/timesfm-forecasting/SKILL.md +785 -0
  791. package/data/skills/tme-immune-profiling-agent/SKILL.md +220 -0
  792. package/data/skills/tooluniverse-adverse-event-detection/SKILL.md +1115 -0
  793. package/data/skills/tooluniverse-antibody-engineering/SKILL.md +1581 -0
  794. package/data/skills/tooluniverse-binder-discovery/SKILL.md +1459 -0
  795. package/data/skills/tooluniverse-cancer-variant-interpretation/SKILL.md +971 -0
  796. package/data/skills/tooluniverse-chemical-compound-retrieval/SKILL.md +322 -0
  797. package/data/skills/tooluniverse-chemical-safety/SKILL.md +733 -0
  798. package/data/skills/tooluniverse-clinical-guidelines/SKILL.md +399 -0
  799. package/data/skills/tooluniverse-clinical-trial-design/SKILL.md +1195 -0
  800. package/data/skills/tooluniverse-clinical-trial-matching/SKILL.md +1333 -0
  801. package/data/skills/tooluniverse-crispr-screen-analysis/SKILL.md +900 -0
  802. package/data/skills/tooluniverse-disease-research/SKILL.md +630 -0
  803. package/data/skills/tooluniverse-drug-drug-interaction/SKILL.md +73 -0
  804. package/data/skills/tooluniverse-drug-repurposing/SKILL.md +595 -0
  805. package/data/skills/tooluniverse-drug-research/SKILL.md +1642 -0
  806. package/data/skills/tooluniverse-drug-target-validation/SKILL.md +1206 -0
  807. package/data/skills/tooluniverse-epigenomics/SKILL.md +1489 -0
  808. package/data/skills/tooluniverse-expression-data-retrieval/SKILL.md +389 -0
  809. package/data/skills/tooluniverse-gene-enrichment/SKILL.md +402 -0
  810. package/data/skills/tooluniverse-gwas-drug-discovery/SKILL.md +576 -0
  811. package/data/skills/tooluniverse-gwas-finemapping/SKILL.md +309 -0
  812. package/data/skills/tooluniverse-gwas-snp-interpretation/SKILL.md +223 -0
  813. package/data/skills/tooluniverse-gwas-study-explorer/SKILL.md +342 -0
  814. package/data/skills/tooluniverse-gwas-trait-to-gene/SKILL.md +236 -0
  815. package/data/skills/tooluniverse-image-analysis/SKILL.md +439 -0
  816. package/data/skills/tooluniverse-immune-repertoire-analysis/SKILL.md +949 -0
  817. package/data/skills/tooluniverse-immunotherapy-response-prediction/SKILL.md +865 -0
  818. package/data/skills/tooluniverse-infectious-disease/SKILL.md +749 -0
  819. package/data/skills/tooluniverse-literature-deep-research/SKILL.md +1050 -0
  820. package/data/skills/tooluniverse-metabolomics/SKILL.md +298 -0
  821. package/data/skills/tooluniverse-metabolomics-analysis/SKILL.md +764 -0
  822. package/data/skills/tooluniverse-multi-omics-integration/SKILL.md +703 -0
  823. package/data/skills/tooluniverse-multiomic-disease-characterization/SKILL.md +1138 -0
  824. package/data/skills/tooluniverse-network-pharmacology/SKILL.md +1312 -0
  825. package/data/skills/tooluniverse-pharmacovigilance/SKILL.md +807 -0
  826. package/data/skills/tooluniverse-phylogenetics/SKILL.md +461 -0
  827. package/data/skills/tooluniverse-polygenic-risk-score/SKILL.md +397 -0
  828. package/data/skills/tooluniverse-precision-medicine-stratification/SKILL.md +1143 -0
  829. package/data/skills/tooluniverse-precision-oncology/SKILL.md +1091 -0
  830. package/data/skills/tooluniverse-protein-interactions/SKILL.md +446 -0
  831. package/data/skills/tooluniverse-protein-structure-retrieval/SKILL.md +416 -0
  832. package/data/skills/tooluniverse-protein-therapeutic-design/SKILL.md +637 -0
  833. package/data/skills/tooluniverse-proteomics-analysis/SKILL.md +843 -0
  834. package/data/skills/tooluniverse-rare-disease-diagnosis/SKILL.md +1257 -0
  835. package/data/skills/tooluniverse-rnaseq-deseq2/SKILL.md +536 -0
  836. package/data/skills/tooluniverse-sequence-retrieval/SKILL.md +419 -0
  837. package/data/skills/tooluniverse-single-cell/SKILL.md +719 -0
  838. package/data/skills/tooluniverse-spatial-omics-analysis/SKILL.md +1102 -0
  839. package/data/skills/tooluniverse-spatial-transcriptomics/SKILL.md +788 -0
  840. package/data/skills/tooluniverse-statistical-modeling/SKILL.md +557 -0
  841. package/data/skills/tooluniverse-structural-variant-analysis/SKILL.md +1356 -0
  842. package/data/skills/tooluniverse-systems-biology/SKILL.md +374 -0
  843. package/data/skills/tooluniverse-target-research/SKILL.md +1510 -0
  844. package/data/skills/tooluniverse-variant-analysis/SKILL.md +448 -0
  845. package/data/skills/tooluniverse-variant-interpretation/SKILL.md +1118 -0
  846. package/data/skills/torch-geometric/SKILL.md +674 -0
  847. package/data/skills/torch_geometric/SKILL.md +670 -0
  848. package/data/skills/torchdrug/SKILL.md +444 -0
  849. package/data/skills/tpd-ternary-complex-agent/SKILL.md +226 -0
  850. package/data/skills/transformers/SKILL.md +157 -0
  851. package/data/skills/travel-health-analyzer/SKILL.md +421 -0
  852. package/data/skills/treatment-plans/SKILL.md +1576 -0
  853. package/data/skills/trial-eligibility-agent/SKILL.md +54 -0
  854. package/data/skills/trialgpt-matching/SKILL.md +66 -0
  855. package/data/skills/tumor-clonal-evolution-agent/SKILL.md +134 -0
  856. package/data/skills/tumor-heterogeneity-agent/SKILL.md +216 -0
  857. package/data/skills/tumor-mutational-burden-agent/SKILL.md +188 -0
  858. package/data/skills/ukb-navigator/SKILL.md +113 -0
  859. package/data/skills/umap-learn/SKILL.md +473 -0
  860. package/data/skills/uniprot-database/SKILL.md +189 -0
  861. package/data/skills/universal-single-cell-annotator/SKILL.md +72 -0
  862. package/data/skills/using-git-worktrees/SKILL.md +218 -0
  863. package/data/skills/using-superpowers/SKILL.md +95 -0
  864. package/data/skills/usmle/SKILL.md +62 -0
  865. package/data/skills/uspto-database/SKILL.md +597 -0
  866. package/data/skills/vaex/SKILL.md +180 -0
  867. package/data/skills/varcadd-pathogenicity/SKILL.md +68 -0
  868. package/data/skills/variant-interpretation-acmg/SKILL.md +58 -0
  869. package/data/skills/variant-interpretation-acmg/bioSkills/clinical-interpretation/SKILL.md +334 -0
  870. package/data/skills/variant-interpretation-acmg/bioSkills/consensus-sequences/SKILL.md +343 -0
  871. package/data/skills/variant-interpretation-acmg/bioSkills/deepvariant/SKILL.md +279 -0
  872. package/data/skills/variant-interpretation-acmg/bioSkills/filtering-best-practices/SKILL.md +362 -0
  873. package/data/skills/variant-interpretation-acmg/bioSkills/gatk-variant-calling/SKILL.md +398 -0
  874. package/data/skills/variant-interpretation-acmg/bioSkills/joint-calling/SKILL.md +343 -0
  875. package/data/skills/variant-interpretation-acmg/bioSkills/structural-variant-calling/SKILL.md +256 -0
  876. package/data/skills/variant-interpretation-acmg/bioSkills/variant-annotation/SKILL.md +387 -0
  877. package/data/skills/variant-interpretation-acmg/bioSkills/variant-calling/SKILL.md +258 -0
  878. package/data/skills/variant-interpretation-acmg/bioSkills/variant-normalization/SKILL.md +304 -0
  879. package/data/skills/variant-interpretation-acmg/bioSkills/vcf-basics/SKILL.md +329 -0
  880. package/data/skills/variant-interpretation-acmg/bioSkills/vcf-manipulation/SKILL.md +398 -0
  881. package/data/skills/variant-interpretation-acmg/bioSkills/vcf-statistics/SKILL.md +424 -0
  882. package/data/skills/variant-interpretation-acmg/varCADD/SKILL.md +68 -0
  883. package/data/skills/vcf-annotator/SKILL.md +55 -0
  884. package/data/skills/verification-before-completion/SKILL.md +139 -0
  885. package/data/skills/virtual-lab-agent/SKILL.md +240 -0
  886. package/data/skills/wearable-analysis-agent/SKILL.md +70 -0
  887. package/data/skills/weightloss-analyzer/SKILL.md +320 -0
  888. package/data/skills/wellally-tech/SKILL.md +685 -0
  889. package/data/skills/wikipedia-search/SKILL.md +481 -0
  890. package/data/skills/writing-plans/SKILL.md +116 -0
  891. package/data/skills/writing-skills/SKILL.md +655 -0
  892. package/data/skills/xlsx/SKILL.md +292 -0
  893. package/data/skills/xlsx-official/SKILL.md +289 -0
  894. package/data/skills/zarr-python/SKILL.md +777 -0
  895. package/data/skills/zinc-database/SKILL.md +398 -0
  896. package/data/tools/__init__.py +8 -0
  897. package/data/tools/hpc.py +71 -0
  898. package/data/tools/hpc_client/__init__.py +8 -0
  899. package/data/tools/hpc_client/builders/__init__.py +12 -0
  900. package/data/tools/hpc_client/builders/alphafold.py +36 -0
  901. package/data/tools/hpc_client/builders/boltz.py +33 -0
  902. package/data/tools/hpc_client/builders/chai.py +30 -0
  903. package/data/tools/hpc_client/builders/immunebuilder.py +31 -0
  904. package/data/tools/hpc_client/builders/rfantibody.py +58 -0
  905. package/data/tools/hpc_client/builders/thermompnn.py +16 -0
  906. package/data/tools/hpc_client/hpc_api.py +41 -0
  907. package/data/tools/hpc_client/hpc_tools.py +218 -0
  908. package/data/tools/hpc_dynamic.py +71 -0
  909. package/data/tools/integrations/__init__.py +14 -0
  910. package/data/tools/integrations/adaptyv.py +107 -0
  911. package/data/tools/integrations/addgene.py +52 -0
  912. package/data/tools/integrations/api_internal.py +33 -0
  913. package/data/tools/molecular_biology.py +688 -0
  914. package/data/tools/pharmacology.py +67 -0
  915. package/data/workflows/bulk-omics-clustering/SKILL.md +501 -0
  916. package/data/workflows/bulk-omics-clustering/references/best_practices.md +395 -0
  917. package/data/workflows/bulk-omics-clustering/references/clustering_methods_comparison.md +288 -0
  918. package/data/workflows/bulk-omics-clustering/references/common-patterns.md +1136 -0
  919. package/data/workflows/bulk-omics-clustering/references/decision-guide.md +819 -0
  920. package/data/workflows/bulk-omics-clustering/references/distance_metrics_guide.md +388 -0
  921. package/data/workflows/bulk-omics-clustering/references/parameter_guide.md +396 -0
  922. package/data/workflows/bulk-omics-clustering/references/r-quick-start.md +105 -0
  923. package/data/workflows/bulk-omics-clustering/references/validation_metrics_guide.md +315 -0
  924. package/data/workflows/bulk-omics-clustering/scripts/characterize_clusters.py +255 -0
  925. package/data/workflows/bulk-omics-clustering/scripts/cluster_validation.py +449 -0
  926. package/data/workflows/bulk-omics-clustering/scripts/density_clustering.py +321 -0
  927. package/data/workflows/bulk-omics-clustering/scripts/dimensionality_reduction.py +328 -0
  928. package/data/workflows/bulk-omics-clustering/scripts/distance_metrics.py +251 -0
  929. package/data/workflows/bulk-omics-clustering/scripts/export_results.py +456 -0
  930. package/data/workflows/bulk-omics-clustering/scripts/hierarchical_clustering.R +229 -0
  931. package/data/workflows/bulk-omics-clustering/scripts/hierarchical_clustering.py +269 -0
  932. package/data/workflows/bulk-omics-clustering/scripts/kmeans_clustering.py +346 -0
  933. package/data/workflows/bulk-omics-clustering/scripts/load_example_data.R +171 -0
  934. package/data/workflows/bulk-omics-clustering/scripts/load_example_data.py +171 -0
  935. package/data/workflows/bulk-omics-clustering/scripts/model_based_clustering.py +370 -0
  936. package/data/workflows/bulk-omics-clustering/scripts/optimal_clusters.py +381 -0
  937. package/data/workflows/bulk-omics-clustering/scripts/plot_cluster_heatmap.R +141 -0
  938. package/data/workflows/bulk-omics-clustering/scripts/plot_clustering_results.py +452 -0
  939. package/data/workflows/bulk-omics-clustering/scripts/prepare_data.py +250 -0
  940. package/data/workflows/bulk-omics-clustering/scripts/stability_analysis.py +434 -0
  941. package/data/workflows/bulk-rnaseq-counts-to-de-deseq2/SKILL.md +505 -0
  942. package/data/workflows/bulk-rnaseq-counts-to-de-deseq2/references/comprehensive-reference.md +440 -0
  943. package/data/workflows/bulk-rnaseq-counts-to-de-deseq2/references/decision-guide.md +327 -0
  944. package/data/workflows/bulk-rnaseq-counts-to-de-deseq2/references/troubleshooting.md +456 -0
  945. package/data/workflows/bulk-rnaseq-counts-to-de-deseq2/references/usage-guide.md +75 -0
  946. package/data/workflows/bulk-rnaseq-counts-to-de-deseq2/scripts/basic_workflow.R +149 -0
  947. package/data/workflows/bulk-rnaseq-counts-to-de-deseq2/scripts/batch_correction.R +44 -0
  948. package/data/workflows/bulk-rnaseq-counts-to-de-deseq2/scripts/export_results.R +190 -0
  949. package/data/workflows/bulk-rnaseq-counts-to-de-deseq2/scripts/extract_results.R +242 -0
  950. package/data/workflows/bulk-rnaseq-counts-to-de-deseq2/scripts/load_example_data.R +250 -0
  951. package/data/workflows/bulk-rnaseq-counts-to-de-deseq2/scripts/multi_condition.R +50 -0
  952. package/data/workflows/bulk-rnaseq-counts-to-de-deseq2/scripts/qc_plots.R +410 -0
  953. package/data/workflows/bulk-rnaseq-counts-to-de-deseq2/scripts/transformations.R +218 -0
  954. package/data/workflows/chip-atlas-diff-analysis/SKILL.md +222 -0
  955. package/data/workflows/chip-atlas-diff-analysis/references/chipatlas_diff_api_format.md +106 -0
  956. package/data/workflows/chip-atlas-diff-analysis/references/diff_analysis_methods.md +89 -0
  957. package/data/workflows/chip-atlas-diff-analysis/references/output_format.md +78 -0
  958. package/data/workflows/chip-atlas-diff-analysis/scripts/__init__.py +1 -0
  959. package/data/workflows/chip-atlas-diff-analysis/scripts/annotate_genes.py +144 -0
  960. package/data/workflows/chip-atlas-diff-analysis/scripts/export_all.py +498 -0
  961. package/data/workflows/chip-atlas-diff-analysis/scripts/filter_regions.py +176 -0
  962. package/data/workflows/chip-atlas-diff-analysis/scripts/generate_all_plots.py +321 -0
  963. package/data/workflows/chip-atlas-diff-analysis/scripts/load_example_data.py +149 -0
  964. package/data/workflows/chip-atlas-diff-analysis/scripts/load_user_data.py +211 -0
  965. package/data/workflows/chip-atlas-diff-analysis/scripts/parse_bed_results.py +240 -0
  966. package/data/workflows/chip-atlas-diff-analysis/scripts/qc_checks.py +621 -0
  967. package/data/workflows/chip-atlas-diff-analysis/scripts/query_chipatlas_api.py +329 -0
  968. package/data/workflows/chip-atlas-diff-analysis/scripts/run_diff_workflow.py +256 -0
  969. package/data/workflows/chip-atlas-peak-enrichment/SKILL.md +212 -0
  970. package/data/workflows/chip-atlas-peak-enrichment/references/chipatlas_metadata_format.md +115 -0
  971. package/data/workflows/chip-atlas-peak-enrichment/references/enrichment_statistics.md +145 -0
  972. package/data/workflows/chip-atlas-peak-enrichment/references/peak_thresholds.md +63 -0
  973. package/data/workflows/chip-atlas-peak-enrichment/references/promoter_definitions.md +69 -0
  974. package/data/workflows/chip-atlas-peak-enrichment/scripts/__init__.py +1 -0
  975. package/data/workflows/chip-atlas-peak-enrichment/scripts/convert_genes_to_regions.py +271 -0
  976. package/data/workflows/chip-atlas-peak-enrichment/scripts/export_all.py +456 -0
  977. package/data/workflows/chip-atlas-peak-enrichment/scripts/filter_experiments.py +116 -0
  978. package/data/workflows/chip-atlas-peak-enrichment/scripts/generate_all_plots.py +280 -0
  979. package/data/workflows/chip-atlas-peak-enrichment/scripts/load_example_data.py +96 -0
  980. package/data/workflows/chip-atlas-peak-enrichment/scripts/load_user_data.py +183 -0
  981. package/data/workflows/chip-atlas-peak-enrichment/scripts/query_chipatlas_api.py +349 -0
  982. package/data/workflows/chip-atlas-peak-enrichment/scripts/run_enrichment_workflow.py +271 -0
  983. package/data/workflows/chip-atlas-target-genes/SKILL.md +230 -0
  984. package/data/workflows/chip-atlas-target-genes/references/macs2_binding_scores.md +89 -0
  985. package/data/workflows/chip-atlas-target-genes/references/string_scores.md +58 -0
  986. package/data/workflows/chip-atlas-target-genes/references/target_genes_data_format.md +73 -0
  987. package/data/workflows/chip-atlas-target-genes/scripts/__init__.py +0 -0
  988. package/data/workflows/chip-atlas-target-genes/scripts/download_target_genes.py +200 -0
  989. package/data/workflows/chip-atlas-target-genes/scripts/export_all.py +340 -0
  990. package/data/workflows/chip-atlas-target-genes/scripts/filter_targets.py +205 -0
  991. package/data/workflows/chip-atlas-target-genes/scripts/generate_all_plots.py +330 -0
  992. package/data/workflows/chip-atlas-target-genes/scripts/load_example_query.py +61 -0
  993. package/data/workflows/chip-atlas-target-genes/scripts/load_user_query.py +47 -0
  994. package/data/workflows/chip-atlas-target-genes/scripts/run_target_genes_workflow.py +141 -0
  995. package/data/workflows/clinicaltrials-landscape/SKILL.md +257 -0
  996. package/data/workflows/clinicaltrials-landscape/references/api-parameters.md +181 -0
  997. package/data/workflows/clinicaltrials-landscape/references/mechanisms.md +141 -0
  998. package/data/workflows/clinicaltrials-landscape/references/output-schema.md +184 -0
  999. package/data/workflows/clinicaltrials-landscape/scripts/__init__.py +1 -0
  1000. package/data/workflows/clinicaltrials-landscape/scripts/classify_mechanisms.py +359 -0
  1001. package/data/workflows/clinicaltrials-landscape/scripts/compile_trials.py +579 -0
  1002. package/data/workflows/clinicaltrials-landscape/scripts/disease_config.py +161 -0
  1003. package/data/workflows/clinicaltrials-landscape/scripts/export_all.py +242 -0
  1004. package/data/workflows/clinicaltrials-landscape/scripts/generate_landscape_plots.py +761 -0
  1005. package/data/workflows/clinicaltrials-landscape/scripts/generate_pdf_report.py +1465 -0
  1006. package/data/workflows/clinicaltrials-landscape/scripts/generate_report.py +1813 -0
  1007. package/data/workflows/clinicaltrials-landscape/scripts/query_clinicaltrials.py +307 -0
  1008. package/data/workflows/coexpression-network/SKILL.md +344 -0
  1009. package/data/workflows/coexpression-network/references/parameter-tuning-guide.md +591 -0
  1010. package/data/workflows/coexpression-network/references/troubleshooting.md +483 -0
  1011. package/data/workflows/coexpression-network/references/wgcna-best-practices.md +563 -0
  1012. package/data/workflows/coexpression-network/references/wgcna-reference.md +538 -0
  1013. package/data/workflows/coexpression-network/scripts/build_network.R +43 -0
  1014. package/data/workflows/coexpression-network/scripts/correlate_modules_traits.R +92 -0
  1015. package/data/workflows/coexpression-network/scripts/export_wgcna_results.R +117 -0
  1016. package/data/workflows/coexpression-network/scripts/identify_hub_genes.R +63 -0
  1017. package/data/workflows/coexpression-network/scripts/load_example_data.R +214 -0
  1018. package/data/workflows/coexpression-network/scripts/module_enrichment.R +159 -0
  1019. package/data/workflows/coexpression-network/scripts/pick_soft_power.R +70 -0
  1020. package/data/workflows/coexpression-network/scripts/plot_all_wgcna.R +104 -0
  1021. package/data/workflows/coexpression-network/scripts/plot_eigengene_heatmap.R +65 -0
  1022. package/data/workflows/coexpression-network/scripts/plot_hub_genes.R +70 -0
  1023. package/data/workflows/coexpression-network/scripts/plot_module_dendrogram.R +50 -0
  1024. package/data/workflows/coexpression-network/scripts/plotting_helpers.R +87 -0
  1025. package/data/workflows/coexpression-network/scripts/prepare_wgcna_data.R +73 -0
  1026. package/data/workflows/coexpression-network/scripts/wgcna_workflow.R +93 -0
  1027. package/data/workflows/experimental-design-statistics/SKILL.md +408 -0
  1028. package/data/workflows/experimental-design-statistics/references/batch_effect_mitigation.md +756 -0
  1029. package/data/workflows/experimental-design-statistics/references/cv_tissue_database.csv +30 -0
  1030. package/data/workflows/experimental-design-statistics/references/experimental_design_best_practices.md +515 -0
  1031. package/data/workflows/experimental-design-statistics/references/multiple_testing_guide.md +730 -0
  1032. package/data/workflows/experimental-design-statistics/references/power_analysis_guidelines.md +635 -0
  1033. package/data/workflows/experimental-design-statistics/references/qc_guidelines.md +310 -0
  1034. package/data/workflows/experimental-design-statistics/references/software_requirements.md +328 -0
  1035. package/data/workflows/experimental-design-statistics/references/troubleshooting_guide.md +510 -0
  1036. package/data/workflows/experimental-design-statistics/scripts/batch_assignment.R +302 -0
  1037. package/data/workflows/experimental-design-statistics/scripts/batch_validation.R +342 -0
  1038. package/data/workflows/experimental-design-statistics/scripts/export_design.R +352 -0
  1039. package/data/workflows/experimental-design-statistics/scripts/load_example_data.R +204 -0
  1040. package/data/workflows/experimental-design-statistics/scripts/multiple_testing.R +417 -0
  1041. package/data/workflows/experimental-design-statistics/scripts/plot_power_curves.R +317 -0
  1042. package/data/workflows/experimental-design-statistics/scripts/power_atacseq.R +229 -0
  1043. package/data/workflows/experimental-design-statistics/scripts/power_pilot_based.R +289 -0
  1044. package/data/workflows/experimental-design-statistics/scripts/power_rnaseq.R +247 -0
  1045. package/data/workflows/experimental-design-statistics/scripts/sample_size_de.R +327 -0
  1046. package/data/workflows/experimental-design-statistics/scripts/sample_size_scrna.R +304 -0
  1047. package/data/workflows/functional-enrichment-from-degs/SKILL.md +387 -0
  1048. package/data/workflows/functional-enrichment-from-degs/references/database_guide.md +354 -0
  1049. package/data/workflows/functional-enrichment-from-degs/references/decision-guide.md +546 -0
  1050. package/data/workflows/functional-enrichment-from-degs/references/gsea_ora_comparison.md +213 -0
  1051. package/data/workflows/functional-enrichment-from-degs/references/gsea_ora_validation_framework.md +483 -0
  1052. package/data/workflows/functional-enrichment-from-degs/references/interpretation_guidelines.md +374 -0
  1053. package/data/workflows/functional-enrichment-from-degs/references/method-reference.md +742 -0
  1054. package/data/workflows/functional-enrichment-from-degs/scripts/export_results.R +190 -0
  1055. package/data/workflows/functional-enrichment-from-degs/scripts/generate_plots.R +240 -0
  1056. package/data/workflows/functional-enrichment-from-degs/scripts/get_msigdb_genesets.R +75 -0
  1057. package/data/workflows/functional-enrichment-from-degs/scripts/load_de_results.R +60 -0
  1058. package/data/workflows/functional-enrichment-from-degs/scripts/load_example_data.R +212 -0
  1059. package/data/workflows/functional-enrichment-from-degs/scripts/prepare_gene_lists.R +92 -0
  1060. package/data/workflows/functional-enrichment-from-degs/scripts/run_gsea.R +44 -0
  1061. package/data/workflows/functional-enrichment-from-degs/scripts/run_ora.R +53 -0
  1062. package/data/workflows/genetic-variant-annotation/SKILL.md +440 -0
  1063. package/data/workflows/genetic-variant-annotation/references/auto_installation_implementation.md +274 -0
  1064. package/data/workflows/genetic-variant-annotation/references/consequence_terms.md +392 -0
  1065. package/data/workflows/genetic-variant-annotation/references/filtering_strategies.md +808 -0
  1066. package/data/workflows/genetic-variant-annotation/references/installation_guide.md +557 -0
  1067. package/data/workflows/genetic-variant-annotation/references/pathogenicity_interpretation.md +473 -0
  1068. package/data/workflows/genetic-variant-annotation/references/qc_guidelines.md +524 -0
  1069. package/data/workflows/genetic-variant-annotation/references/snpeff_best_practices.md +481 -0
  1070. package/data/workflows/genetic-variant-annotation/references/tool_selection_guide.md +433 -0
  1071. package/data/workflows/genetic-variant-annotation/references/troubleshooting_guide.md +678 -0
  1072. package/data/workflows/genetic-variant-annotation/references/vep_best_practices.md +450 -0
  1073. package/data/workflows/genetic-variant-annotation/scripts/annotate_genes.py +243 -0
  1074. package/data/workflows/genetic-variant-annotation/scripts/export_results.py +450 -0
  1075. package/data/workflows/genetic-variant-annotation/scripts/filter_variants.py +365 -0
  1076. package/data/workflows/genetic-variant-annotation/scripts/install_tools.py +246 -0
  1077. package/data/workflows/genetic-variant-annotation/scripts/load_example_data.py +166 -0
  1078. package/data/workflows/genetic-variant-annotation/scripts/parse_snpeff_output.py +283 -0
  1079. package/data/workflows/genetic-variant-annotation/scripts/parse_vep_output.py +257 -0
  1080. package/data/workflows/genetic-variant-annotation/scripts/plot_variant_distribution.py +372 -0
  1081. package/data/workflows/genetic-variant-annotation/scripts/prioritize_variants.py +287 -0
  1082. package/data/workflows/genetic-variant-annotation/scripts/run_snpeff.py +418 -0
  1083. package/data/workflows/genetic-variant-annotation/scripts/run_vep.py +358 -0
  1084. package/data/workflows/genetic-variant-annotation/scripts/select_tool.py +203 -0
  1085. package/data/workflows/genetic-variant-annotation/scripts/test_complete_workflow.py +312 -0
  1086. package/data/workflows/genetic-variant-annotation/scripts/test_pickle_load.py +118 -0
  1087. package/data/workflows/genetic-variant-annotation/scripts/validate_vcf.py +351 -0
  1088. package/data/workflows/genetic-variant-annotation/scripts/verify_changes.py +212 -0
  1089. package/data/workflows/grn-pyscenic/SKILL.md +331 -0
  1090. package/data/workflows/grn-pyscenic/references/cli_interface.md +222 -0
  1091. package/data/workflows/grn-pyscenic/references/database_downloads.md +245 -0
  1092. package/data/workflows/grn-pyscenic/scripts/export_all.py +192 -0
  1093. package/data/workflows/grn-pyscenic/scripts/generate_report.py +512 -0
  1094. package/data/workflows/grn-pyscenic/scripts/integrate_with_adata.py +54 -0
  1095. package/data/workflows/grn-pyscenic/scripts/load_example_data.py +200 -0
  1096. package/data/workflows/grn-pyscenic/scripts/load_expression_data.py +61 -0
  1097. package/data/workflows/grn-pyscenic/scripts/plot_regulon_visualizations.py +263 -0
  1098. package/data/workflows/grn-pyscenic/scripts/run_grn_workflow.py +184 -0
  1099. package/data/workflows/gwas-to-function-twas/SKILL.md +394 -0
  1100. package/data/workflows/gwas-to-function-twas/references/fusion_best_practices.md +120 -0
  1101. package/data/workflows/gwas-to-function-twas/references/installation-guide.md +414 -0
  1102. package/data/workflows/gwas-to-function-twas/references/ldsc_qc_guidelines.md +287 -0
  1103. package/data/workflows/gwas-to-function-twas/references/spredixxcan_best_practices.md +166 -0
  1104. package/data/workflows/gwas-to-function-twas/references/therapeutic_interpretation_guide.md +717 -0
  1105. package/data/workflows/gwas-to-function-twas/references/tissue_reference_guide.md +182 -0
  1106. package/data/workflows/gwas-to-function-twas/references/troubleshooting_guide.md +317 -0
  1107. package/data/workflows/gwas-to-function-twas/references/twas_hub_validation_guide.md +88 -0
  1108. package/data/workflows/gwas-to-function-twas/scripts/colocalization_analysis.py +187 -0
  1109. package/data/workflows/gwas-to-function-twas/scripts/druggability_scoring.py +199 -0
  1110. package/data/workflows/gwas-to-function-twas/scripts/export_results.py +220 -0
  1111. package/data/workflows/gwas-to-function-twas/scripts/integrate_variant_annotation.py +194 -0
  1112. package/data/workflows/gwas-to-function-twas/scripts/interpret_therapeutic_direction.py +418 -0
  1113. package/data/workflows/gwas-to-function-twas/scripts/mendelian_randomization.py +749 -0
  1114. package/data/workflows/gwas-to-function-twas/scripts/multilayer_direction_analysis.py +471 -0
  1115. package/data/workflows/gwas-to-function-twas/scripts/plot_twas_results.py +252 -0
  1116. package/data/workflows/gwas-to-function-twas/scripts/run_fusion.py +155 -0
  1117. package/data/workflows/gwas-to-function-twas/scripts/run_smultixcan.py +102 -0
  1118. package/data/workflows/gwas-to-function-twas/scripts/run_spredixxcan.py +138 -0
  1119. package/data/workflows/gwas-to-function-twas/scripts/select_reference_panel.py +253 -0
  1120. package/data/workflows/gwas-to-function-twas/scripts/validate_gwas_sumstats.py +214 -0
  1121. package/data/workflows/gwas-to-function-twas/scripts/validate_with_twas_hub.py +439 -0
  1122. package/data/workflows/lasso-biomarker-panel/SKILL.md +322 -0
  1123. package/data/workflows/lasso-biomarker-panel/references/decision-guide.md +64 -0
  1124. package/data/workflows/lasso-biomarker-panel/references/lasso-reference.md +110 -0
  1125. package/data/workflows/lasso-biomarker-panel/references/validation-guide.md +105 -0
  1126. package/data/workflows/lasso-biomarker-panel/scripts/biological_interpretation.R +1560 -0
  1127. package/data/workflows/lasso-biomarker-panel/scripts/biomarker_plots.R +350 -0
  1128. package/data/workflows/lasso-biomarker-panel/scripts/export_results.R +1492 -0
  1129. package/data/workflows/lasso-biomarker-panel/scripts/lasso_workflow.R +328 -0
  1130. package/data/workflows/lasso-biomarker-panel/scripts/load_example_data.R +1903 -0
  1131. package/data/workflows/lasso-biomarker-panel/scripts/plotting_helpers.R +78 -0
  1132. package/data/workflows/lasso-biomarker-panel/scripts/prepare_features.R +225 -0
  1133. package/data/workflows/lasso-biomarker-panel/scripts/query_cellxgene.py +107 -0
  1134. package/data/workflows/lasso-biomarker-panel/scripts/validate_external.R +174 -0
  1135. package/data/workflows/literature-preclinical/SKILL.md +276 -0
  1136. package/data/workflows/literature-preclinical/assets/eval/simple_test.py +386 -0
  1137. package/data/workflows/literature-preclinical/references/experiment-extraction-guide.md +147 -0
  1138. package/data/workflows/literature-preclinical/references/full-text-enrichment-guide.md +121 -0
  1139. package/data/workflows/literature-preclinical/references/preclinical-search-guide.md +117 -0
  1140. package/data/workflows/literature-preclinical/scripts/extract_experiments.py +401 -0
  1141. package/data/workflows/literature-preclinical/scripts/generate_plots.R +303 -0
  1142. package/data/workflows/literature-preclinical/scripts/narrative_synthesis.py +653 -0
  1143. package/data/workflows/literature-preclinical/scripts/preclinical_search.py +332 -0
  1144. package/data/workflows/literature-preclinical/scripts/preclinical_synthesis.py +237 -0
  1145. package/data/workflows/literature-preclinical/scripts/report_generation.py +326 -0
  1146. package/data/workflows/mendelian-randomization-twosamplemr/SKILL.md +210 -0
  1147. package/data/workflows/mendelian-randomization-twosamplemr/references/interpretation-guide.md +239 -0
  1148. package/data/workflows/mendelian-randomization-twosamplemr/references/method-reference.md +190 -0
  1149. package/data/workflows/mendelian-randomization-twosamplemr/scripts/export_results.R +123 -0
  1150. package/data/workflows/mendelian-randomization-twosamplemr/scripts/generate_report.R +411 -0
  1151. package/data/workflows/mendelian-randomization-twosamplemr/scripts/load_data.R +281 -0
  1152. package/data/workflows/mendelian-randomization-twosamplemr/scripts/mr_plots.R +163 -0
  1153. package/data/workflows/mendelian-randomization-twosamplemr/scripts/run_mr_analysis.R +322 -0
  1154. package/data/workflows/pcr-primer-design/SKILL.md +397 -0
  1155. package/data/workflows/pcr-primer-design/references/code_examples.md +594 -0
  1156. package/data/workflows/pcr-primer-design/references/miqe_guidelines.md +453 -0
  1157. package/data/workflows/pcr-primer-design/references/parameter_ranges.md +356 -0
  1158. package/data/workflows/pcr-primer-design/references/primer_design_best_practices.md +451 -0
  1159. package/data/workflows/pcr-primer-design/references/troubleshooting_guide.md +477 -0
  1160. package/data/workflows/pcr-primer-design/scripts/__init__.py +2 -0
  1161. package/data/workflows/pcr-primer-design/scripts/calculate_tm.py +306 -0
  1162. package/data/workflows/pcr-primer-design/scripts/check_dimers.py +298 -0
  1163. package/data/workflows/pcr-primer-design/scripts/check_secondary_structures.py +343 -0
  1164. package/data/workflows/pcr-primer-design/scripts/design_qpcr_primers.py +233 -0
  1165. package/data/workflows/pcr-primer-design/scripts/design_standard_primers.py +197 -0
  1166. package/data/workflows/pcr-primer-design/scripts/design_taqman_probes.py +226 -0
  1167. package/data/workflows/pcr-primer-design/scripts/export_results.py +382 -0
  1168. package/data/workflows/pcr-primer-design/scripts/generate_reports.py +379 -0
  1169. package/data/workflows/pcr-primer-design/scripts/validate_specificity.py +311 -0
  1170. package/data/workflows/pcr-primer-design/scripts/visualize_primers.py +379 -0
  1171. package/data/workflows/polygenic-risk-score-prs-catalog/SKILL.md +195 -0
  1172. package/data/workflows/polygenic-risk-score-prs-catalog/references/interpretation-guide.md +80 -0
  1173. package/data/workflows/polygenic-risk-score-prs-catalog/references/pgs-catalog-guide.md +109 -0
  1174. package/data/workflows/polygenic-risk-score-prs-catalog/scripts/export_results.R +186 -0
  1175. package/data/workflows/polygenic-risk-score-prs-catalog/scripts/generate_plots.R +283 -0
  1176. package/data/workflows/polygenic-risk-score-prs-catalog/scripts/load_pgs_weights.R +228 -0
  1177. package/data/workflows/polygenic-risk-score-prs-catalog/scripts/load_reference_data.R +191 -0
  1178. package/data/workflows/polygenic-risk-score-prs-catalog/scripts/score_traits.R +216 -0
  1179. package/data/workflows/pooled-crispr-screens/SKILL.md +362 -0
  1180. package/data/workflows/pooled-crispr-screens/references/crispr_screen_best_practices.md +349 -0
  1181. package/data/workflows/pooled-crispr-screens/references/qc_guidelines.md +722 -0
  1182. package/data/workflows/pooled-crispr-screens/references/statistical_methods.md +644 -0
  1183. package/data/workflows/pooled-crispr-screens/references/troubleshooting_guide.md +684 -0
  1184. package/data/workflows/pooled-crispr-screens/references/umi_optimization.md +297 -0
  1185. package/data/workflows/pooled-crispr-screens/scripts/concatenate_libraries.py +132 -0
  1186. package/data/workflows/pooled-crispr-screens/scripts/detect_perturbed_cells.py +255 -0
  1187. package/data/workflows/pooled-crispr-screens/scripts/differential_expression.py +202 -0
  1188. package/data/workflows/pooled-crispr-screens/scripts/differential_expression_glmgampoi.py +320 -0
  1189. package/data/workflows/pooled-crispr-screens/scripts/export_results.py +261 -0
  1190. package/data/workflows/pooled-crispr-screens/scripts/expression_filtering.py +159 -0
  1191. package/data/workflows/pooled-crispr-screens/scripts/gene_name_corrections.py +188 -0
  1192. package/data/workflows/pooled-crispr-screens/scripts/generate_report.py +485 -0
  1193. package/data/workflows/pooled-crispr-screens/scripts/load_10x_libraries.py +69 -0
  1194. package/data/workflows/pooled-crispr-screens/scripts/load_example_data.py +257 -0
  1195. package/data/workflows/pooled-crispr-screens/scripts/map_sgrna_to_cells.py +119 -0
  1196. package/data/workflows/pooled-crispr-screens/scripts/normalize_and_scale.py +140 -0
  1197. package/data/workflows/pooled-crispr-screens/scripts/qc_filtering.py +185 -0
  1198. package/data/workflows/pooled-crispr-screens/scripts/run_glmgampoi.R +181 -0
  1199. package/data/workflows/pooled-crispr-screens/scripts/screen_all_perturbations.py +306 -0
  1200. package/data/workflows/pooled-crispr-screens/scripts/validate_perturbations.py +314 -0
  1201. package/data/workflows/pooled-crispr-screens/scripts/visualize_perturbations.py +314 -0
  1202. package/data/workflows/scrnaseq-scanpy-core-analysis/SKILL.md +425 -0
  1203. package/data/workflows/scrnaseq-scanpy-core-analysis/references/ambient_rna_correction.md +422 -0
  1204. package/data/workflows/scrnaseq-scanpy-core-analysis/references/common-patterns.md +533 -0
  1205. package/data/workflows/scrnaseq-scanpy-core-analysis/references/integration_methods.md +820 -0
  1206. package/data/workflows/scrnaseq-scanpy-core-analysis/references/marker_gene_database.md +471 -0
  1207. package/data/workflows/scrnaseq-scanpy-core-analysis/references/pseudobulk_de_guide.md +408 -0
  1208. package/data/workflows/scrnaseq-scanpy-core-analysis/references/qc_guidelines.md +535 -0
  1209. package/data/workflows/scrnaseq-scanpy-core-analysis/references/scanpy_best_practices.md +496 -0
  1210. package/data/workflows/scrnaseq-scanpy-core-analysis/references/troubleshooting_guide.md +668 -0
  1211. package/data/workflows/scrnaseq-scanpy-core-analysis/references/workflow-details.md +727 -0
  1212. package/data/workflows/scrnaseq-scanpy-core-analysis/scripts/annotate_celltypes.py +431 -0
  1213. package/data/workflows/scrnaseq-scanpy-core-analysis/scripts/cluster_cells.py +293 -0
  1214. package/data/workflows/scrnaseq-scanpy-core-analysis/scripts/export_results.py +423 -0
  1215. package/data/workflows/scrnaseq-scanpy-core-analysis/scripts/filter_cells.py +531 -0
  1216. package/data/workflows/scrnaseq-scanpy-core-analysis/scripts/find_markers.py +391 -0
  1217. package/data/workflows/scrnaseq-scanpy-core-analysis/scripts/find_variable_genes.py +222 -0
  1218. package/data/workflows/scrnaseq-scanpy-core-analysis/scripts/integrate_scvi.py +665 -0
  1219. package/data/workflows/scrnaseq-scanpy-core-analysis/scripts/integration_diagnostics.py +678 -0
  1220. package/data/workflows/scrnaseq-scanpy-core-analysis/scripts/load_example_data.py +68 -0
  1221. package/data/workflows/scrnaseq-scanpy-core-analysis/scripts/normalize_data.py +325 -0
  1222. package/data/workflows/scrnaseq-scanpy-core-analysis/scripts/plot_dimreduction.py +389 -0
  1223. package/data/workflows/scrnaseq-scanpy-core-analysis/scripts/plot_qc.py +320 -0
  1224. package/data/workflows/scrnaseq-scanpy-core-analysis/scripts/pseudobulk_de.py +553 -0
  1225. package/data/workflows/scrnaseq-scanpy-core-analysis/scripts/qc_metrics.py +477 -0
  1226. package/data/workflows/scrnaseq-scanpy-core-analysis/scripts/remove_ambient_rna.py +347 -0
  1227. package/data/workflows/scrnaseq-scanpy-core-analysis/scripts/run_umap.py +188 -0
  1228. package/data/workflows/scrnaseq-scanpy-core-analysis/scripts/scale_and_pca.py +365 -0
  1229. package/data/workflows/scrnaseq-scanpy-core-analysis/scripts/setup_and_import.py +334 -0
  1230. package/data/workflows/scrnaseq-seurat-core-analysis/SKILL.md +585 -0
  1231. package/data/workflows/scrnaseq-seurat-core-analysis/references/ambient_rna_correction.md +422 -0
  1232. package/data/workflows/scrnaseq-seurat-core-analysis/references/common-patterns.md +667 -0
  1233. package/data/workflows/scrnaseq-seurat-core-analysis/references/decision-guide.md +456 -0
  1234. package/data/workflows/scrnaseq-seurat-core-analysis/references/integration_methods.md +864 -0
  1235. package/data/workflows/scrnaseq-seurat-core-analysis/references/marker_gene_database.md +471 -0
  1236. package/data/workflows/scrnaseq-seurat-core-analysis/references/pseudobulk_de_guide.md +408 -0
  1237. package/data/workflows/scrnaseq-seurat-core-analysis/references/qc_guidelines.md +452 -0
  1238. package/data/workflows/scrnaseq-seurat-core-analysis/references/seurat_best_practices.md +417 -0
  1239. package/data/workflows/scrnaseq-seurat-core-analysis/references/troubleshooting_guide.md +566 -0
  1240. package/data/workflows/scrnaseq-seurat-core-analysis/references/workflow-details.md +801 -0
  1241. package/data/workflows/scrnaseq-seurat-core-analysis/scripts/annotate_celltypes.R +306 -0
  1242. package/data/workflows/scrnaseq-seurat-core-analysis/scripts/cluster_cells.R +223 -0
  1243. package/data/workflows/scrnaseq-seurat-core-analysis/scripts/export_results.R +292 -0
  1244. package/data/workflows/scrnaseq-seurat-core-analysis/scripts/filter_cells.R +576 -0
  1245. package/data/workflows/scrnaseq-seurat-core-analysis/scripts/find_markers.R +325 -0
  1246. package/data/workflows/scrnaseq-seurat-core-analysis/scripts/find_variable_features.R +106 -0
  1247. package/data/workflows/scrnaseq-seurat-core-analysis/scripts/integrate_batches.R +504 -0
  1248. package/data/workflows/scrnaseq-seurat-core-analysis/scripts/integration_diagnostics.R +596 -0
  1249. package/data/workflows/scrnaseq-seurat-core-analysis/scripts/load_example_data.R +89 -0
  1250. package/data/workflows/scrnaseq-seurat-core-analysis/scripts/normalize_data.R +184 -0
  1251. package/data/workflows/scrnaseq-seurat-core-analysis/scripts/plot_dimreduction.R +273 -0
  1252. package/data/workflows/scrnaseq-seurat-core-analysis/scripts/plot_qc.R +250 -0
  1253. package/data/workflows/scrnaseq-seurat-core-analysis/scripts/pseudobulk_de.R +324 -0
  1254. package/data/workflows/scrnaseq-seurat-core-analysis/scripts/qc_metrics.R +358 -0
  1255. package/data/workflows/scrnaseq-seurat-core-analysis/scripts/remove_ambient_rna.R +281 -0
  1256. package/data/workflows/scrnaseq-seurat-core-analysis/scripts/run_umap.R +116 -0
  1257. package/data/workflows/scrnaseq-seurat-core-analysis/scripts/scale_and_pca.R +243 -0
  1258. package/data/workflows/scrnaseq-seurat-core-analysis/scripts/setup_and_import.R +193 -0
  1259. package/data/workflows/spatial-transcriptomics/SKILL.md +256 -0
  1260. package/data/workflows/spatial-transcriptomics/references/spatial-analysis-guide.md +216 -0
  1261. package/data/workflows/spatial-transcriptomics/scripts/export_results.py +214 -0
  1262. package/data/workflows/spatial-transcriptomics/scripts/generate_all_plots.py +397 -0
  1263. package/data/workflows/spatial-transcriptomics/scripts/load_example_data.py +175 -0
  1264. package/data/workflows/spatial-transcriptomics/scripts/spatial_workflow.py +206 -0
  1265. package/dist/bgi.js +28 -1
  1266. package/package.json +2 -1
@@ -0,0 +1,775 @@
1
+ ---
2
+ name: nutrition-analyzer
3
+ description: 分析营养数据、识别营养模式、评估营养状况,并提供个性化营养建议。支持与运动、睡眠、慢性病数据的关联分析。
4
+ allowed-tools: Read, Grep, Glob, Write
5
+ ---
6
+
7
+ # 营养分析器技能
8
+
9
+ 分析饮食和营养数据,识别营养模式,评估营养状况,并提供个性化营养改善建议。
10
+
11
+ ## 功能
12
+
13
+ ### 1. 营养趋势分析
14
+
15
+ 分析营养素摄入的变化趋势,识别改善或需要关注的方面。
16
+
17
+ **分析维度**:
18
+ - 宏量营养素趋势(蛋白质、碳水、脂肪、纤维、卡路里)
19
+ - 微量营养素趋势(维生素、矿物质)
20
+ - 热量来源分布变化
21
+ - 餐食模式(饮食时间、频率)
22
+ - 食物类别偏好
23
+
24
+ **输出**:
25
+ - 趋势方向(改善/稳定/下降)
26
+ - 变化幅度和百分比
27
+ - 趋势显著性
28
+ - 改进建议
29
+
30
+ ### 2. 营养素摄入评估
31
+
32
+ 评估营养素摄入是否达到推荐标准(RDA/AI)。
33
+
34
+ **评估内容**:
35
+ - **宏量营养素评估**:
36
+ - 蛋白质摄入量和质量
37
+ - 碳水化合物类型分布(精制 vs 复杂碳水)
38
+ - 脂肪类型分布(饱和/单不饱和/多不饱和/反式脂肪)
39
+ - 膳食纤维摄入量
40
+
41
+ - **维生素评估**:
42
+ - 维生素A、C、D、E、K
43
+ - 维生素B族(B1、B2、B3、B6、B12、叶酸、泛酸、生物素)
44
+ - 与RDA对比
45
+ - 缺乏风险评估
46
+
47
+ - **矿物质评估**:
48
+ - 常量矿物质:钙、磷、镁、钠、钾、氯、硫
49
+ - 微量矿物质:铁、锌、铜、锰、碘、硒、铬、钼
50
+ - 与RDA对比
51
+ - 缺乏风险评估
52
+
53
+ - **特殊营养素评估**:
54
+ - Omega-3脂肪酸(EPA、DHA、ALA)
55
+ - 胆碱
56
+ - 辅酶Q10
57
+ - 植物化学物(类黄酮、类胡萝卜素等)
58
+
59
+ **输出**:
60
+ - 每种营养素的达成率
61
+ - 缺乏/不足/充足/过量分级
62
+ - 缺乏风险识别
63
+ - 优先改善建议
64
+
65
+ ### 3. 营养状况评估
66
+
67
+ 综合评估用户的营养状况。
68
+
69
+ **评估内容**:
70
+ - **整体营养质量评分**:
71
+ - 营养密度评分
72
+ - 食物多样性评分
73
+ - 均衡饮食评分
74
+
75
+ - **营养模式识别**:
76
+ - 饮食模式类型(地中海式、DASH、素食等)
77
+ - 饮食时间模式(进食频率、进食窗口)
78
+ - 零食和加餐模式
79
+
80
+ - **营养风险识别**:
81
+ - 营养缺乏风险(如维生素D缺乏、铁缺乏)
82
+ - 营养过量风险(如维生素A过量、钠过量)
83
+ - 不健康饮食习惯(高糖、高脂、高钠)
84
+
85
+ **输出**:
86
+ - 营养状况等级(优秀/良好/一般/较差)
87
+ - 主要营养问题识别
88
+ - 风险因素列表
89
+ - 改善优先级
90
+
91
+ ### 4. 相关性分析
92
+
93
+ 分析营养与其他健康指标的相关性。
94
+
95
+ **支持的相关性分析**:
96
+ - **营养 ↔ 体重**:
97
+ - 卡路里摄入与体重变化的关系
98
+ - 宏量营养素比例与体重管理
99
+ - 进食时间与代谢关系
100
+
101
+ - **营养 ↔ 运动**:
102
+ - 营养摄入对运动表现的影响
103
+ - 运动日vs休息日的营养需求
104
+ - 蛋白质摄入与肌肉恢复
105
+
106
+ - **营养 ↔ 睡眠**:
107
+ - 咖啡因摄入与睡眠质量
108
+ - 晚餐时间与入睡时间
109
+ - 特定营养素(如镁、色氨酸)与睡眠
110
+
111
+ - **营养 ↔ 血压**:
112
+ - 钠摄入与血压
113
+ - 钾/钠比值与血压
114
+ - DASH饮食依从性与血压控制
115
+
116
+ - **营养 ↔ 血糖**:
117
+ - 碳水化合物类型与血糖波动
118
+ - 膳食纤维与血糖控制
119
+ - 进食时间与血糖曲线
120
+
121
+ **输出**:
122
+ - 相关系数(-1到1)
123
+ - 相关性强度(弱/中/强)
124
+ - 统计显著性
125
+ - 因果关系推断
126
+ - 实践建议
127
+
128
+ ### 5. 个性化建议生成
129
+
130
+ 基于用户数据生成个性化营养改善建议。
131
+
132
+ **建议类型**:
133
+ - **营养素调整建议**:
134
+ - 增加缺乏的营养素
135
+ - 减少过量的营养素
136
+ - 优化营养素比例
137
+
138
+ - **食物选择建议**:
139
+ - 推荐特定食物类别
140
+ - 食物替换建议(更健康的选择)
141
+ - 食物搭配建议(促进吸收)
142
+
143
+ - **饮食习惯建议**:
144
+ - 进食时间调整
145
+ - 餐食频率调整
146
+ - 烹饪方式建议
147
+
148
+ - **补充剂建议**(仅供参考):
149
+ - 基于缺乏风险的补充剂建议
150
+ - 补充剂剂量和时机
151
+ - 相互作用警示
152
+
153
+ **建议依据**:
154
+ - DRIs/RDA标准
155
+ - 用户营养历史数据
156
+ - 用户健康状况和目标
157
+ - 循证营养学证据
158
+
159
+ ---
160
+
161
+ ## 使用说明
162
+
163
+ ### 触发条件
164
+
165
+ 当用户请求以下内容时触发本技能:
166
+ - 营养趋势分析
167
+ - 营养素摄入评估
168
+ - 营养状况评估
169
+ - 营养改善建议
170
+ - 营养与其他健康指标的关联分析
171
+
172
+ ### 执行步骤
173
+
174
+ #### 步骤 1: 确定分析范围
175
+
176
+ 明确用户请求的分析类型和时间范围:
177
+ - 分析类型:趋势/评估/相关性/建议
178
+ - 时间范围:周/月/季度/自定义
179
+ - 分析深度:宏量营养素/微量营养素/全面分析
180
+
181
+ #### 步骤 2: 读取数据
182
+
183
+ **主要数据源**:
184
+ 1. `data-example/nutrition-tracker.json` - 营养追踪主数据
185
+ 2. `data-example/nutrition-logs/YYYY-MM/YYYY-MM-DD.json` - 每日饮食记录
186
+
187
+ **关联数据源**:
188
+ 1. `data-example/profile.json` - 体重、BMI等基础数据
189
+ 2. `data-example/fitness-tracker.json` - 运动数据
190
+ 3. `data-example/sleep-tracker.json` - 睡眠数据
191
+ 4. `data-example/hypertension-tracker.json` - 血压数据
192
+ 5. `data-example/diabetes-tracker.json` - 血糖数据
193
+
194
+ #### 步骤 3: 数据分析
195
+
196
+ 根据分析类型执行相应的分析算法:
197
+
198
+ **趋势分析算法**:
199
+ - 线性回归计算趋势斜率
200
+ - 移动平均平滑波动
201
+ - 统计显著性检验
202
+
203
+ **RDA达成率计算**:
204
+ ```python
205
+ rda_achievement = (actual_intake / rda_value) * 100
206
+
207
+ status_classification:
208
+ - < 50%: 严重缺乏
209
+ - 50-75%: 不足
210
+ - 75-100%: 接近目标
211
+ - 100-150%: 充足(理想范围)
212
+ - > 150%: 过量(注意安全上限UL)
213
+ ```
214
+
215
+ **营养密度评分**:
216
+ ```python
217
+ nutrient_density_score = (
218
+ (vitamins_achieved / total_vitamins) * 40 +
219
+ (minerals_achieved / total_minerals) * 30 +
220
+ (fiber_achieved / fiber_rda) * 30
221
+ )
222
+ ```
223
+
224
+ **相关性分析算法**:
225
+ - Pearson相关系数计算
226
+ - 滞后相关性分析(考虑时间延迟效应)
227
+ - 多变量回归分析
228
+
229
+ #### 步骤 4: 生成报告
230
+
231
+ 按照标准格式输出分析报告(见"输出格式"部分)
232
+
233
+ ---
234
+
235
+ ## 输出格式
236
+
237
+ ### 营养趋势分析报告
238
+
239
+ ```markdown
240
+ # 营养摄入趋势分析报告
241
+
242
+ ## 分析周期
243
+ 2025-03-20 至 2025-06-20(3个月,90天记录)
244
+
245
+ ## 宏量营养素趋势
246
+
247
+ ### 卡路里摄入
248
+ - **趋势**:⬇️ 下降
249
+ - **开始**:平均2100卡/天
250
+ - **当前**:平均1950卡/天
251
+ - **变化**:-150卡/天 (-7.1%)
252
+ - **解读**:卡路里摄入适度减少,与减重目标一致
253
+
254
+ **趋势线**:
255
+ ```
256
+ 2100 ┤ ╭╮
257
+ 2050 ┤ ╭╯╰╮
258
+ 2000 ┼─╯ ╰╮
259
+ 1950 ┤ ╰
260
+ 1900 └───────────
261
+ 3月 4月 5月 6月
262
+ ```
263
+
264
+ ### 蛋白质
265
+ - **趋势**:➡️ 稳定
266
+ - **平均**:82g/天(范围:70-95g)
267
+ - **目标**:80g/天
268
+ - **达标率**:93%(84/90天达标)
269
+ - **解读**:蛋白质摄入稳定,基本达标
270
+
271
+ ### 膳食纤维
272
+ - **趋势**:⬆️ 改善
273
+ - **开始**:平均18g/天
274
+ - **当前**:平均22g/天
275
+ - **变化**:+4g/天 (+22%)
276
+ - **目标**:30g/天
277
+ - **解读**:纤维摄入显著增加,但仍需继续努力
278
+
279
+ ### 脂肪
280
+ - **趋势**:⬇️ 下降
281
+ - **开始**:平均75g/天
282
+ - **当前**:平均68g/天
283
+ - **变化**:-7g/天 (-9.3%)
284
+ - **目标**:≤65g/天
285
+ - **解读**:脂肪摄入减少,接近目标
286
+
287
+ **脂肪类型分布变化**:
288
+ | 脂肪类型 | 开始 | 当前 | 目标 | 趋势 |
289
+ |---------|------|------|------|------|
290
+ | 饱和脂肪 | 25g | 20g | <20g | ⬇️ 改善 |
291
+ | 单不饱和 | 30g | 32g | >35g | ⬆️ 略增 |
292
+ | 多不饱和 | 15g | 12g | 15-20g | ⬇️ 需增加 |
293
+ | 反式脂肪 | 2g | 0.5g | 0g | ⬇️ 改善 |
294
+
295
+ ## 维生素状况趋势
296
+
297
+ ### 维生素D
298
+ - **摄入趋势**:⬆️ 增加(补充剂开始)
299
+ - **开始**:平均2μg/天(饮食来源)
300
+ - **当前**:平均52μg/天(含2000IU补充剂)
301
+ - **RDA**:15μg/天
302
+ - **血清水平变化**:
303
+ - 基线(2025-05):18 ng/mL
304
+ - 当前(2025-06):22 ng/mL
305
+ - 目标:30-100 ng/mL
306
+ - **解读**:✅ 补充剂起效,但需继续监测
307
+
308
+ ### 维生素C
309
+ - **趋势**:⬆️ 改善
310
+ - **开始**:平均65mg/天
311
+ - **当前**:平均85mg/天
312
+ - **RDA**:100mg/天
313
+ - **达标率**:从65% → 85%
314
+ - **建议**:增加柑橘类、奇异果、草莓等水果
315
+
316
+ ### B族维生素
317
+ - **维生素B12**:✅ 充足(平均2.5μg,RDA 2.4μg)
318
+ - **叶酸**:⚠️ 不足(平均320μg,RDA 400μg)
319
+ - **B6**:✅ 充足(平均1.5mg,RDA 1.3mg)
320
+
321
+ ## 矿物质趋势
322
+
323
+ ### 钙
324
+ - **趋势**:➡️ 稳定
325
+ - **平均**:850mg/天
326
+ - **RDA**:1000mg/天
327
+ - **达标率**:85%
328
+ - **主要来源**:乳制品40%、豆腐25%、绿叶蔬菜20%
329
+
330
+ ### 铁
331
+ - **趋势**:✅ 充足
332
+ - **平均**:12mg/天
333
+ - **RDA**:8mg/天(男性)
334
+ - **达标率**:150%
335
+ - **主要来源**:肉类、蛋类、豆类、绿叶蔬菜
336
+
337
+ ### 钠
338
+ - **趋势**:⬇️ 改善
339
+ - **开始**:平均2800mg/天
340
+ - **当前**:平均2100mg/天
341
+ - **目标**:<2300mg/天(理想<1500mg)
342
+ - **解读**:✅ 达到一般目标,⚠️ 理想目标仍需努力
343
+
344
+ ### 钾
345
+ - **趋势**:⬆️ 改善
346
+ - **开始**:平均2800mg/天
347
+ - **当前**:平均3200mg/天
348
+ - **目标**:3500-4700mg/天
349
+ - **钾/钠比值**:从1.0 → 1.5(目标>2)
350
+ - **建议**:继续增加水果和蔬菜
351
+
352
+ ## 特殊营养素趋势
353
+
354
+ ### Omega-3
355
+ - **趋势**:⬆️ 增加(鱼油补充剂)
356
+ - **开始**:平均150mg/天
357
+ - **当前**:平均850mg/天(含补充剂)
358
+ - **推荐量**:500-1000mg/天
359
+ - **状态**:✅ 达标
360
+
361
+ ### 胆碱
362
+ - **趋势**:➡️ 稳定
363
+ - **平均**:350mg/天
364
+ - **AI(适宜摄入量)**:425mg/天
365
+ - **达标率**:82%
366
+ - **主要来源**:鸡蛋(60%)、肉类(25%)、豆类(15%)
367
+
368
+ ## 饮食模式分析
369
+
370
+ ### 食物类别分布
371
+ | 食物类别 | 占比 | 变化 | 评价 |
372
+ |---------|------|------|------|
373
+ | 蔬菜水果 | 35% | +8% | ✅ 增加 |
374
+ | 全谷物 | 20% | +5% | ✅ 改善 |
375
+ | 精制谷物 | 15% | -7% | ✅ 减少 |
376
+ | 蛋白质来源 | 20% | 稳定 | ✅ 充足 |
377
+ | 添加脂肪 | 8% | -3% | ✅ 减少 |
378
+ | 添加糖 | 2% | -2% | ✅ 减少 |
379
+
380
+ ### 进食时间模式
381
+ - **平均进食窗口**:12.5小时(07:30 - 20:00)
382
+ - **进食频率**:平均4.2次/天
383
+ - **最常见餐食时间**:
384
+ - 早餐:07:30(90%天数)
385
+ - 午餐:12:15(95%天数)
386
+ - 晚餐:18:45(98%天数)
387
+ - 加餐:15:30(60%天数)
388
+
389
+ ### 饮食质量评分
390
+ - **营养密度评分**:7.2/10(从6.5提升)
391
+ - **食物多样性评分**:6.8/10
392
+ - **均衡饮食评分**:7.5/10
393
+ - **综合评分**:7.2/10 → **良好**
394
+
395
+ ## 洞察与建议
396
+
397
+ ### 关键洞察
398
+
399
+ 1. **膳食纤维持续改善但仍不足**
400
+ - 从18g增至22g,但仍低于目标30g
401
+ - 影响:饱腹感、肠道健康、血糖控制
402
+ - 建议:每餐至少包含5g纤维
403
+
404
+ 2. **脂肪质量改善**
405
+ - 饱和脂肪减少,反式脂肪几乎消除
406
+ - 多不饱和脂肪略低,需增加Omega-3食物
407
+ - 建议:增加深海鱼类、坚果、亚麻籽
408
+
409
+ 3. **钠摄入改善但钾/钠比仍低**
410
+ - 钠减少33%,钾增加14%
411
+ - 钾/钠比从1.0升至1.5,仍低于目标2.0
412
+ - 建议:继续增加高钾食物(香蕉、橙子、土豆、菠菜)
413
+
414
+ 4. **维生素D补充剂有效**
415
+ - 血清水平从18升至22 ng/mL(4周+4ng)
416
+ - 预计3-4个月可达目标范围
417
+ - 建议:继续补充,定期监测
418
+
419
+ ### 优先级行动计划
420
+
421
+ #### Priority 1:提升膳食纤维至30g/天(2周)
422
+
423
+ **具体行动**:
424
+ 1. 早餐:全谷物(燕麦/全麦面包)+ 水果(9g)
425
+ 2. 午餐:糙米/全麦面 + 2份蔬菜(8g)
426
+ 3. 晚餐:红薯/杂粮 + 2份蔬菜(8g)
427
+ 4. 加餐:水果 + 坚果(5g)
428
+ **总计**:30g ✅
429
+
430
+ #### Priority 2:优化钾/钠比值至2.0(4周)
431
+
432
+ **具体行动**:
433
+ 1. 减少加工食品(主要钠源)
434
+ 2. 每日2-3份高钾水果(香蕉、橙子、猕猴桃)
435
+ 3. 蔬菜选择菠菜、土豆、蘑菇、番茄
436
+ 4. 使用香料替代盐调味
437
+
438
+ #### Priority 3:维持维生素D补充(长期)
439
+
440
+ **监测计划**:
441
+ - 3个月后复查血清水平
442
+ - 目标:40-60 ng/mL
443
+ - 根据结果调整剂量
444
+
445
+ ## 营养目标进度
446
+
447
+ | 目标 | 开始 | 当前 | 目标值 | 进度 | 状态 |
448
+ |------|------|------|--------|------|------|
449
+ | 卡路里 | 2100 | 1950 | 1800-2000 | 100% | ✅ 达标 |
450
+ | 蛋白质 | 75g | 82g | 80g | 100% | ✅ 达标 |
451
+ | 膳食纤维 | 18g | 22g | 30g | 73% | ⚠️ 进行中 |
452
+ | 维生素D | 18 ng/mL | 22 ng/mL | 30-100 | 20% | ⚠️ 改善中 |
453
+ | 钠摄入 | 2800mg | 2100mg | <2300 | 100% | ✅ 达标 |
454
+ | Omega-3 | 150mg | 850mg | 500-1000mg | 100% | ✅ 达标 |
455
+
456
+ ---
457
+
458
+ **报告生成时间**:2025-06-20
459
+ **分析周期**:2025-03-20 至 2025-06-20(90天)
460
+ **数据记录数**:90天
461
+ **营养分析器版本**:v1.0
462
+ ```
463
+
464
+ ---
465
+
466
+ ## 数据结构
467
+
468
+ ### 饮食记录数据
469
+
470
+ ```json
471
+ {
472
+ "date": "2025-06-20",
473
+ "meals": [
474
+ {
475
+ "type": "breakfast",
476
+ "time": "07:30",
477
+ "foods": ["鸡蛋", "牛奶", "全麦面包"],
478
+ "calories": 450,
479
+ "macronutrients": {
480
+ "protein_g": 20,
481
+ "carbs_g": 55,
482
+ "fat_g": 15,
483
+ "fiber_g": 5,
484
+ "saturated_fat_g": 5,
485
+ "monounsaturated_fat_g": 6,
486
+ "polyunsaturated_fat_g": 3,
487
+ "trans_fat_g": 0.1
488
+ },
489
+ "micronutrients": {
490
+ "vitamin_a_mcg": 150,
491
+ "vitamin_c_mg": 5,
492
+ "vitamin_d_mcg": 1.5,
493
+ "vitamin_e_mg": 1,
494
+ "vitamin_k_mcg": 5,
495
+ "thiamine_mg": 0.3,
496
+ "riboflavin_mg": 0.4,
497
+ "niacin_mg": 4,
498
+ "vitamin_b6_mg": 0.1,
499
+ "folate_mcg": 30,
500
+ "vitamin_b12_mcg": 0.6,
501
+ "calcium_mg": 250,
502
+ "iron_mg": 2,
503
+ "magnesium_mg": 40,
504
+ "phosphorus_mg": 200,
505
+ "zinc_mg": 2,
506
+ "selenium_mcg": 10,
507
+ "potassium_mg": 350,
508
+ "sodium_mg": 300
509
+ },
510
+ "special_nutrients": {
511
+ "omega_3_g": 0.1,
512
+ "choline_mg": 150
513
+ }
514
+ }
515
+ ],
516
+ "daily_summary": {
517
+ "total_calories": 2000,
518
+ "total_macronutrients": {
519
+ "protein_g": 80,
520
+ "carbs_g": 250,
521
+ "fat_g": 65,
522
+ "fiber_g": 30
523
+ },
524
+ "rda_achievement": {
525
+ "protein": 100,
526
+ "vitamin_c": 85,
527
+ "vitamin_d": 35,
528
+ "calcium": 90,
529
+ "iron": 75
530
+ },
531
+ "goal_achieved": true
532
+ }
533
+ }
534
+ ```
535
+
536
+ ---
537
+
538
+ ## 算法说明
539
+
540
+ ### RDA达成率计算
541
+
542
+ ```python
543
+ def calculate_rda_achievement(actual_intake, rda_value, ul_value=None):
544
+ """
545
+ 计算RDA达成率和状态
546
+
547
+ 参数:
548
+ - actual_intake: 实际摄入量
549
+ - rda_value: 推荐膳食供给量
550
+ - ul_value: 可耐受最高摄入量(可选)
551
+
552
+ 返回:
553
+ - achievement_rate: 达成率百分比
554
+ - status: 状态标签
555
+ """
556
+ achievement_rate = (actual_intake / rda_value) * 100
557
+
558
+ if ul_value and actual_intake > ul_value:
559
+ status = "exceeds_ul"
560
+ category = "过量(危险)"
561
+ elif achievement_rate < 50:
562
+ status = "severe_deficiency"
563
+ category = "严重缺乏"
564
+ elif achievement_rate < 75:
565
+ status = "insufficient"
566
+ category = "不足"
567
+ elif achievement_rate < 100:
568
+ status = "approaching_target"
569
+ category = "接近目标"
570
+ elif achievement_rate <= 150:
571
+ status = "adequate"
572
+ category = "充足"
573
+ else:
574
+ status = "high_intake"
575
+ category = "较高"
576
+
577
+ return {
578
+ 'achievement_rate': round(achievement_rate, 1),
579
+ 'status': status,
580
+ 'category': category
581
+ }
582
+ ```
583
+
584
+ ### 营养密度评分
585
+
586
+ ```python
587
+ def calculate_nutrient_density_score(meal_data):
588
+ """
589
+ 计算食物营养密度评分(0-10分)
590
+
591
+ 因素权重:
592
+ - 维生素达成率:40%
593
+ - 矿物质达成率:30%
594
+ - 膳食纤维:20%
595
+ - 限制性营养素(饱和脂肪、钠、添加糖):10%
596
+ """
597
+ score = 0
598
+
599
+ # 维生素评分
600
+ vitamin_achievements = [
601
+ meal_data['micronutrients'][v] / RDA[v]
602
+ for v in ['vitamin_a', 'vitamin_c', 'vitamin_d', 'vitamin_e', 'vitamin_k']
603
+ ]
604
+ vitamin_score = min(sum(vitamin_achievements) / len(vitamin_achievements), 1.5) * 10
605
+ score += min(vitamin_score, 10) * 0.40
606
+
607
+ # 矿物质评分
608
+ mineral_achievements = [
609
+ meal_data['micronutrients'][m] / RDA[m]
610
+ for m in ['calcium', 'iron', 'magnesium', 'zinc']
611
+ ]
612
+ mineral_score = min(sum(mineral_achievements) / len(mineral_achievements), 1.5) * 10
613
+ score += min(mineral_score, 10) * 0.30
614
+
615
+ # 膳食纤维评分
616
+ fiber_score = min(meal_data['macronutrients']['fiber_g'] / 5, 2) * 10
617
+ score += min(fiber_score, 10) * 0.20
618
+
619
+ # 限制性营养素扣分
620
+ penalty = 0
621
+ if meal_data['macronutrients']['saturated_fat_g'] > 10:
622
+ penalty += 2
623
+ if meal_data['micronutrients']['sodium_mg'] > 600:
624
+ penalty += 2
625
+ if meal_data.get('added_sugars_g', 0) > 10:
626
+ penalty += 2
627
+
628
+ score = max(0, score - penalty * 0.10)
629
+
630
+ return round(score, 1)
631
+ ```
632
+
633
+ ### 健康饮食指数评分
634
+
635
+ ```python
636
+ def calculate_healthy_eating_index(daily_data):
637
+ """
638
+ 计算健康饮食指数(HEI-2015改编)
639
+
640
+ 评分范围:0-100分
641
+ """
642
+ score = 0
643
+
644
+ # 充足性成分(满分50分)
645
+ # 1. 水果(5分)
646
+ fruit_servings = daily_data['fruit_servings']
647
+ score += min(fruit_servings, 2.5) * 2
648
+
649
+ # 2. 蔬菜(5分)
650
+ veg_servings = daily_data['vegetable_servings']
651
+ score += min(veg_servings, 3) * 1.67
652
+
653
+ # 3. 全谷物(10分)
654
+ whole_grains_oz = daily_data['whole_grains_oz']
655
+ score += min(whole_grains_oz, 3) * 3.33
656
+
657
+ # 4. 乳制品(10分)
658
+ dairy_servings = daily_data['dairy_servings']
659
+ score += min(dairy_servings, 3) * 3.33
660
+
661
+ # 5. 蛋白质(5分)
662
+ protein_oz = daily_data['protein_oz']
663
+ score += min(protein_oz, 5) * 1
664
+
665
+ # 6. 海鲜/植物蛋白(5分)
666
+ plant_protein_oz = daily_data['plant_protein_oz']
667
+ score += min(plant_protein_oz, 2) * 2.5
668
+
669
+ # 7. 脂肪酸比例(10分)
670
+ fat_ratio = daily_data['unsaturated_fat_g'] / max(daily_data['saturated_fat_g'], 1)
671
+ score += min(fat_ratio, 2.5) * 4
672
+
673
+ # 适度性成分(满分40分,反向计分)
674
+ # 8. 精制谷物(10分,越少越好)
675
+ refined_grains_oz = daily_data['refined_grains_oz']
676
+ score += max(10 - refined_grains_oz * 2, 0)
677
+
678
+ # 9. 钠(10分,越少越好)
679
+ sodium_g = daily_data['sodium_mg'] / 1000
680
+ score += max(10 - sodium_g * 2, 0)
681
+
682
+ # 10. 添加糖(10分,越少越好)
683
+ added_sugars_pct = daily_data['added_sugars_g'] / (daily_data['total_calories'] / 100)
684
+ score += max(10 - added_sugars_pct * 10, 0)
685
+
686
+ # 11. 饱和脂肪(10分,越少越好)
687
+ saturated_fat_pct = daily_data['saturated_fat_g'] / (daily_data['total_calories'] / 100)
688
+ score += max(10 - saturated_fat_pct * 10, 0)
689
+
690
+ return round(score, 1)
691
+ ```
692
+
693
+ ---
694
+
695
+ ## 医学安全边界
696
+
697
+ ⚠️ **重要声明**
698
+
699
+ 本分析仅供健康参考,不构成医疗诊断或营养处方。
700
+
701
+ ### 分析能力范围
702
+
703
+ ✅ **能做到**:
704
+ - 营养数据统计和分析
705
+ - 趋势识别和可视化
706
+ - RDA达成率计算
707
+ - 营养缺乏风险评估
708
+ - 一般性营养建议
709
+ - 补充剂相互作用检查
710
+
711
+ ❌ **不做到**:
712
+ - 诊断营养缺乏疾病
713
+ - 开具补充剂处方
714
+ - 替代注册营养师
715
+ - 处理严重营养不良
716
+ - 评估食物过敏
717
+
718
+ ### 危险信号检测
719
+
720
+ 在分析过程中检测以下危险信号:
721
+
722
+ 1. **营养素过量**:
723
+ - 维生素A > 3000μg(长期)
724
+ - 维生素D > 100μg(长期)
725
+ - 铁 > 45mg(长期)
726
+ - 硒 > 400μg
727
+ - 钠 > 2300mg(持续)
728
+
729
+ 2. **营养素缺乏**:
730
+ - 维生素D < 10μg/天(血清<12 ng/mL)
731
+ - 维生素B12 < 1.5μg/天(素食者)
732
+ - 铁 < 6mg/天(育龄女性)
733
+ - 钙 < 500mg/天
734
+
735
+ 3. **能量摄入异常**:
736
+ - 持续<1200卡/天(可能营养不良)
737
+ - 持续>3500卡/天(可能超重)
738
+
739
+ 4. **饮食模式异常**:
740
+ - 膳食纤维<10g/天
741
+ - 添加糖>25%热量
742
+ - 饱和脂肪>15%热量
743
+
744
+ ### 建议分级
745
+
746
+ **Level 1: 一般性建议**
747
+ - 基于DRIs/RDA标准
748
+ - 适用于一般人群
749
+ - 无需医疗监督
750
+
751
+ **Level 2: 参考性建议**
752
+ - 基于用户数据和健康状况
753
+ - 需结合个人情况
754
+ - 建议咨询营养师
755
+
756
+ **Level 3: 医疗建议**
757
+ - 涉及疾病管理或补充剂
758
+ - 需医生确认
759
+ - 不得自行调整药物剂量
760
+
761
+ ---
762
+
763
+ ## 参考资源
764
+
765
+ - 中国居民膳食营养素参考摄入量 (DRIs):http://www.cnsoc.org/
766
+ - 美国膳食指南:https://www.dietaryguidelines.gov/
767
+ - USDA FoodData Central:https://fooddatacentral.usda.gov/
768
+ - WHO营养建议:https://www.who.int/nutrition/
769
+ - 补充剂相互作用数据库:https://naturalmedicines.therapeuticresearch.com/
770
+
771
+ ---
772
+
773
+ **技能版本**: v1.0
774
+ **创建日期**: 2026-01-06
775
+ **维护者**: WellAlly Tech