@bgicli/bgicli 2.1.1 → 2.2.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (1267) hide show
  1. package/README.md +152 -74
  2. package/data/skills/aav-vector-design-agent/SKILL.md +198 -0
  3. package/data/skills/adaptyv/SKILL.md +112 -0
  4. package/data/skills/adhd-daily-planner/SKILL.md +271 -0
  5. package/data/skills/aeon/SKILL.md +372 -0
  6. package/data/skills/agent-browser/SKILL.md +159 -0
  7. package/data/skills/agentd-drug-discovery/SKILL.md +52 -0
  8. package/data/skills/ai-analyzer/SKILL.md +218 -0
  9. package/data/skills/alphafold/SKILL.md +183 -0
  10. package/data/skills/alphafold-database/SKILL.md +500 -0
  11. package/data/skills/anndata/SKILL.md +394 -0
  12. package/data/skills/antibody-design-agent/SKILL.md +64 -0
  13. package/data/skills/arboreto/SKILL.md +237 -0
  14. package/data/skills/armored-cart-design-agent/SKILL.md +225 -0
  15. package/data/skills/arxiv-search/SKILL.md +224 -0
  16. package/data/skills/autonomous-oncology-agent/SKILL.md +77 -0
  17. package/data/skills/bayesian-optimizer/SKILL.md +60 -0
  18. package/data/skills/benchling-integration/SKILL.md +473 -0
  19. package/data/skills/bgpt-paper-search/SKILL.md +81 -0
  20. package/data/skills/bindcraft/SKILL.md +198 -0
  21. package/data/skills/binder-design/SKILL.md +182 -0
  22. package/data/skills/binding-characterization/SKILL.md +234 -0
  23. package/data/skills/bindingdb-database/SKILL.md +332 -0
  24. package/data/skills/bio-admet-prediction/SKILL.md +224 -0
  25. package/data/skills/bio-alignment-files-bam-statistics/SKILL.md +340 -0
  26. package/data/skills/bio-alignment-filtering/SKILL.md +322 -0
  27. package/data/skills/bio-alignment-indexing/SKILL.md +249 -0
  28. package/data/skills/bio-alignment-io/SKILL.md +301 -0
  29. package/data/skills/bio-alignment-msa-parsing/SKILL.md +366 -0
  30. package/data/skills/bio-alignment-msa-statistics/SKILL.md +375 -0
  31. package/data/skills/bio-alignment-pairwise/SKILL.md +277 -0
  32. package/data/skills/bio-alignment-sorting/SKILL.md +296 -0
  33. package/data/skills/bio-alignment-validation/SKILL.md +374 -0
  34. package/data/skills/bio-atac-seq-atac-peak-calling/SKILL.md +221 -0
  35. package/data/skills/bio-atac-seq-atac-qc/SKILL.md +292 -0
  36. package/data/skills/bio-atac-seq-differential-accessibility/SKILL.md +268 -0
  37. package/data/skills/bio-atac-seq-footprinting/SKILL.md +256 -0
  38. package/data/skills/bio-atac-seq-motif-deviation/SKILL.md +319 -0
  39. package/data/skills/bio-atac-seq-nucleosome-positioning/SKILL.md +321 -0
  40. package/data/skills/bio-basecalling/SKILL.md +368 -0
  41. package/data/skills/bio-batch-downloads/SKILL.md +384 -0
  42. package/data/skills/bio-batch-processing/SKILL.md +303 -0
  43. package/data/skills/bio-bedgraph-handling/SKILL.md +336 -0
  44. package/data/skills/bio-blast-searches/SKILL.md +354 -0
  45. package/data/skills/bio-causal-genomics-colocalization-analysis/SKILL.md +264 -0
  46. package/data/skills/bio-causal-genomics-fine-mapping/SKILL.md +267 -0
  47. package/data/skills/bio-causal-genomics-mediation-analysis/SKILL.md +264 -0
  48. package/data/skills/bio-causal-genomics-mendelian-randomization/SKILL.md +221 -0
  49. package/data/skills/bio-causal-genomics-pleiotropy-detection/SKILL.md +292 -0
  50. package/data/skills/bio-cfdna-preprocessing/SKILL.md +200 -0
  51. package/data/skills/bio-chipseq-differential-binding/SKILL.md +262 -0
  52. package/data/skills/bio-chipseq-motif-analysis/SKILL.md +387 -0
  53. package/data/skills/bio-chipseq-peak-annotation/SKILL.md +239 -0
  54. package/data/skills/bio-chipseq-peak-calling/SKILL.md +277 -0
  55. package/data/skills/bio-chipseq-qc/SKILL.md +391 -0
  56. package/data/skills/bio-chipseq-super-enhancers/SKILL.md +288 -0
  57. package/data/skills/bio-chipseq-visualization/SKILL.md +289 -0
  58. package/data/skills/bio-clinical-databases-clinvar-lookup/SKILL.md +188 -0
  59. package/data/skills/bio-clinical-databases-dbsnp-queries/SKILL.md +171 -0
  60. package/data/skills/bio-clinical-databases-gnomad-frequencies/SKILL.md +205 -0
  61. package/data/skills/bio-clinical-databases-hla-typing/SKILL.md +248 -0
  62. package/data/skills/bio-clinical-databases-myvariant-queries/SKILL.md +174 -0
  63. package/data/skills/bio-clinical-databases-pharmacogenomics/SKILL.md +232 -0
  64. package/data/skills/bio-clinical-databases-polygenic-risk/SKILL.md +276 -0
  65. package/data/skills/bio-clinical-databases-somatic-signatures/SKILL.md +261 -0
  66. package/data/skills/bio-clinical-databases-tumor-mutational-burden/SKILL.md +301 -0
  67. package/data/skills/bio-clinical-databases-variant-prioritization/SKILL.md +225 -0
  68. package/data/skills/bio-clip-seq-binding-site-annotation/SKILL.md +66 -0
  69. package/data/skills/bio-clip-seq-clip-alignment/SKILL.md +70 -0
  70. package/data/skills/bio-clip-seq-clip-motif-analysis/SKILL.md +62 -0
  71. package/data/skills/bio-clip-seq-clip-peak-calling/SKILL.md +282 -0
  72. package/data/skills/bio-clip-seq-clip-preprocessing/SKILL.md +142 -0
  73. package/data/skills/bio-codon-usage/SKILL.md +353 -0
  74. package/data/skills/bio-comparative-genomics-ancestral-reconstruction/SKILL.md +312 -0
  75. package/data/skills/bio-comparative-genomics-hgt-detection/SKILL.md +341 -0
  76. package/data/skills/bio-comparative-genomics-ortholog-inference/SKILL.md +308 -0
  77. package/data/skills/bio-comparative-genomics-positive-selection/SKILL.md +354 -0
  78. package/data/skills/bio-comparative-genomics-synteny-analysis/SKILL.md +315 -0
  79. package/data/skills/bio-compressed-files/SKILL.md +263 -0
  80. package/data/skills/bio-consensus-sequences/SKILL.md +340 -0
  81. package/data/skills/bio-copy-number-cnv-annotation/SKILL.md +307 -0
  82. package/data/skills/bio-copy-number-cnv-visualization/SKILL.md +294 -0
  83. package/data/skills/bio-copy-number-cnvkit-analysis/SKILL.md +290 -0
  84. package/data/skills/bio-copy-number-gatk-cnv/SKILL.md +270 -0
  85. package/data/skills/bio-crispr-screens-base-editing-analysis/SKILL.md +110 -0
  86. package/data/skills/bio-crispr-screens-batch-correction/SKILL.md +316 -0
  87. package/data/skills/bio-crispr-screens-crispresso-editing/SKILL.md +205 -0
  88. package/data/skills/bio-crispr-screens-hit-calling/SKILL.md +264 -0
  89. package/data/skills/bio-crispr-screens-jacks-analysis/SKILL.md +313 -0
  90. package/data/skills/bio-crispr-screens-library-design/SKILL.md +417 -0
  91. package/data/skills/bio-crispr-screens-mageck-analysis/SKILL.md +222 -0
  92. package/data/skills/bio-crispr-screens-screen-qc/SKILL.md +243 -0
  93. package/data/skills/bio-ctdna-mutation-detection/SKILL.md +234 -0
  94. package/data/skills/bio-data-visualization-circos-plots/SKILL.md +405 -0
  95. package/data/skills/bio-data-visualization-color-palettes/SKILL.md +244 -0
  96. package/data/skills/bio-data-visualization-genome-browser-tracks/SKILL.md +328 -0
  97. package/data/skills/bio-data-visualization-genome-tracks/SKILL.md +249 -0
  98. package/data/skills/bio-data-visualization-ggplot2-fundamentals/SKILL.md +313 -0
  99. package/data/skills/bio-data-visualization-heatmaps-clustering/SKILL.md +227 -0
  100. package/data/skills/bio-data-visualization-interactive-visualization/SKILL.md +210 -0
  101. package/data/skills/bio-data-visualization-multipanel-figures/SKILL.md +274 -0
  102. package/data/skills/bio-data-visualization-specialized-omics-plots/SKILL.md +251 -0
  103. package/data/skills/bio-data-visualization-upset-plots/SKILL.md +228 -0
  104. package/data/skills/bio-data-visualization-volcano-customization/SKILL.md +233 -0
  105. package/data/skills/bio-de-deseq2-basics/SKILL.md +376 -0
  106. package/data/skills/bio-de-edger-basics/SKILL.md +418 -0
  107. package/data/skills/bio-de-results/SKILL.md +378 -0
  108. package/data/skills/bio-de-visualization/SKILL.md +408 -0
  109. package/data/skills/bio-differential-expression-batch-correction/SKILL.md +253 -0
  110. package/data/skills/bio-differential-expression-timeseries-de/SKILL.md +370 -0
  111. package/data/skills/bio-differential-splicing/SKILL.md +177 -0
  112. package/data/skills/bio-duplicate-handling/SKILL.md +292 -0
  113. package/data/skills/bio-entrez-fetch/SKILL.md +334 -0
  114. package/data/skills/bio-entrez-link/SKILL.md +325 -0
  115. package/data/skills/bio-entrez-search/SKILL.md +311 -0
  116. package/data/skills/bio-epidemiological-genomics-amr-surveillance/SKILL.md +233 -0
  117. package/data/skills/bio-epidemiological-genomics-pathogen-typing/SKILL.md +202 -0
  118. package/data/skills/bio-epidemiological-genomics-phylodynamics/SKILL.md +207 -0
  119. package/data/skills/bio-epidemiological-genomics-transmission-inference/SKILL.md +237 -0
  120. package/data/skills/bio-epidemiological-genomics-variant-surveillance/SKILL.md +237 -0
  121. package/data/skills/bio-epitranscriptomics-m6a-differential/SKILL.md +88 -0
  122. package/data/skills/bio-epitranscriptomics-m6a-peak-calling/SKILL.md +89 -0
  123. package/data/skills/bio-epitranscriptomics-m6anet-analysis/SKILL.md +101 -0
  124. package/data/skills/bio-epitranscriptomics-merip-preprocessing/SKILL.md +81 -0
  125. package/data/skills/bio-epitranscriptomics-modification-visualization/SKILL.md +98 -0
  126. package/data/skills/bio-experimental-design-batch-design/SKILL.md +110 -0
  127. package/data/skills/bio-experimental-design-multiple-testing/SKILL.md +98 -0
  128. package/data/skills/bio-experimental-design-power-analysis/SKILL.md +84 -0
  129. package/data/skills/bio-experimental-design-sample-size/SKILL.md +93 -0
  130. package/data/skills/bio-expression-matrix-counts-ingest/SKILL.md +220 -0
  131. package/data/skills/bio-expression-matrix-gene-id-mapping/SKILL.md +256 -0
  132. package/data/skills/bio-expression-matrix-metadata-joins/SKILL.md +271 -0
  133. package/data/skills/bio-expression-matrix-sparse-handling/SKILL.md +247 -0
  134. package/data/skills/bio-fastq-quality/SKILL.md +279 -0
  135. package/data/skills/bio-filter-sequences/SKILL.md +265 -0
  136. package/data/skills/bio-flow-cytometry-bead-normalization/SKILL.md +315 -0
  137. package/data/skills/bio-flow-cytometry-clustering-phenotyping/SKILL.md +237 -0
  138. package/data/skills/bio-flow-cytometry-compensation-transformation/SKILL.md +196 -0
  139. package/data/skills/bio-flow-cytometry-cytometry-qc/SKILL.md +382 -0
  140. package/data/skills/bio-flow-cytometry-differential-analysis/SKILL.md +217 -0
  141. package/data/skills/bio-flow-cytometry-doublet-detection/SKILL.md +288 -0
  142. package/data/skills/bio-flow-cytometry-fcs-handling/SKILL.md +221 -0
  143. package/data/skills/bio-flow-cytometry-gating-analysis/SKILL.md +193 -0
  144. package/data/skills/bio-format-conversion/SKILL.md +193 -0
  145. package/data/skills/bio-fragment-analysis/SKILL.md +214 -0
  146. package/data/skills/bio-gatk-variant-calling/SKILL.md +422 -0
  147. package/data/skills/bio-genome-assembly-assembly-polishing/SKILL.md +333 -0
  148. package/data/skills/bio-genome-assembly-assembly-qc/SKILL.md +344 -0
  149. package/data/skills/bio-genome-assembly-contamination-detection/SKILL.md +235 -0
  150. package/data/skills/bio-genome-assembly-hifi-assembly/SKILL.md +178 -0
  151. package/data/skills/bio-genome-assembly-long-read-assembly/SKILL.md +307 -0
  152. package/data/skills/bio-genome-assembly-metagenome-assembly/SKILL.md +227 -0
  153. package/data/skills/bio-genome-assembly-scaffolding/SKILL.md +204 -0
  154. package/data/skills/bio-genome-assembly-short-read-assembly/SKILL.md +319 -0
  155. package/data/skills/bio-genome-engineering-base-editing-design/SKILL.md +277 -0
  156. package/data/skills/bio-genome-engineering-grna-design/SKILL.md +221 -0
  157. package/data/skills/bio-genome-engineering-hdr-template-design/SKILL.md +264 -0
  158. package/data/skills/bio-genome-engineering-off-target-prediction/SKILL.md +232 -0
  159. package/data/skills/bio-genome-engineering-prime-editing-design/SKILL.md +275 -0
  160. package/data/skills/bio-genome-intervals-bed-file-basics/SKILL.md +357 -0
  161. package/data/skills/bio-genome-intervals-bigwig-tracks/SKILL.md +351 -0
  162. package/data/skills/bio-genome-intervals-coverage-analysis/SKILL.md +300 -0
  163. package/data/skills/bio-genome-intervals-gtf-gff-handling/SKILL.md +345 -0
  164. package/data/skills/bio-genome-intervals-interval-arithmetic/SKILL.md +485 -0
  165. package/data/skills/bio-genome-intervals-proximity-operations/SKILL.md +337 -0
  166. package/data/skills/bio-geo-data/SKILL.md +380 -0
  167. package/data/skills/bio-hi-c-analysis-compartment-analysis/SKILL.md +261 -0
  168. package/data/skills/bio-hi-c-analysis-contact-pairs/SKILL.md +278 -0
  169. package/data/skills/bio-hi-c-analysis-hic-data-io/SKILL.md +260 -0
  170. package/data/skills/bio-hi-c-analysis-hic-differential/SKILL.md +328 -0
  171. package/data/skills/bio-hi-c-analysis-hic-visualization/SKILL.md +297 -0
  172. package/data/skills/bio-hi-c-analysis-loop-calling/SKILL.md +284 -0
  173. package/data/skills/bio-hi-c-analysis-matrix-operations/SKILL.md +274 -0
  174. package/data/skills/bio-hi-c-analysis-tad-detection/SKILL.md +239 -0
  175. package/data/skills/bio-imaging-mass-cytometry-cell-segmentation/SKILL.md +241 -0
  176. package/data/skills/bio-imaging-mass-cytometry-data-preprocessing/SKILL.md +279 -0
  177. package/data/skills/bio-imaging-mass-cytometry-interactive-annotation/SKILL.md +304 -0
  178. package/data/skills/bio-imaging-mass-cytometry-phenotyping/SKILL.md +231 -0
  179. package/data/skills/bio-imaging-mass-cytometry-quality-metrics/SKILL.md +316 -0
  180. package/data/skills/bio-imaging-mass-cytometry-spatial-analysis/SKILL.md +246 -0
  181. package/data/skills/bio-immunoinformatics-epitope-prediction/SKILL.md +259 -0
  182. package/data/skills/bio-immunoinformatics-immunogenicity-scoring/SKILL.md +275 -0
  183. package/data/skills/bio-immunoinformatics-mhc-binding-prediction/SKILL.md +260 -0
  184. package/data/skills/bio-immunoinformatics-neoantigen-prediction/SKILL.md +277 -0
  185. package/data/skills/bio-immunoinformatics-tcr-epitope-binding/SKILL.md +257 -0
  186. package/data/skills/bio-isoform-switching/SKILL.md +192 -0
  187. package/data/skills/bio-liquid-biopsy-pipeline/SKILL.md +311 -0
  188. package/data/skills/bio-local-blast/SKILL.md +350 -0
  189. package/data/skills/bio-long-read-sequencing-clair3-variants/SKILL.md +252 -0
  190. package/data/skills/bio-long-read-sequencing-isoseq-analysis/SKILL.md +334 -0
  191. package/data/skills/bio-long-read-sequencing-nanopore-methylation/SKILL.md +110 -0
  192. package/data/skills/bio-longitudinal-monitoring/SKILL.md +271 -0
  193. package/data/skills/bio-longread-alignment/SKILL.md +193 -0
  194. package/data/skills/bio-longread-medaka/SKILL.md +176 -0
  195. package/data/skills/bio-longread-qc/SKILL.md +224 -0
  196. package/data/skills/bio-longread-structural-variants/SKILL.md +201 -0
  197. package/data/skills/bio-machine-learning-atlas-mapping/SKILL.md +139 -0
  198. package/data/skills/bio-machine-learning-biomarker-discovery/SKILL.md +157 -0
  199. package/data/skills/bio-machine-learning-model-validation/SKILL.md +148 -0
  200. package/data/skills/bio-machine-learning-omics-classifiers/SKILL.md +146 -0
  201. package/data/skills/bio-machine-learning-prediction-explanation/SKILL.md +162 -0
  202. package/data/skills/bio-machine-learning-survival-analysis/SKILL.md +176 -0
  203. package/data/skills/bio-metabolomics-lipidomics/SKILL.md +265 -0
  204. package/data/skills/bio-metabolomics-metabolite-annotation/SKILL.md +241 -0
  205. package/data/skills/bio-metabolomics-msdial-preprocessing/SKILL.md +308 -0
  206. package/data/skills/bio-metabolomics-normalization-qc/SKILL.md +283 -0
  207. package/data/skills/bio-metabolomics-pathway-mapping/SKILL.md +237 -0
  208. package/data/skills/bio-metabolomics-statistical-analysis/SKILL.md +276 -0
  209. package/data/skills/bio-metabolomics-targeted-analysis/SKILL.md +314 -0
  210. package/data/skills/bio-metabolomics-xcms-preprocessing/SKILL.md +268 -0
  211. package/data/skills/bio-metagenomics-abundance/SKILL.md +203 -0
  212. package/data/skills/bio-metagenomics-amr-detection/SKILL.md +293 -0
  213. package/data/skills/bio-metagenomics-functional-profiling/SKILL.md +252 -0
  214. package/data/skills/bio-metagenomics-kraken/SKILL.md +204 -0
  215. package/data/skills/bio-metagenomics-metaphlan/SKILL.md +214 -0
  216. package/data/skills/bio-metagenomics-strain-tracking/SKILL.md +292 -0
  217. package/data/skills/bio-metagenomics-visualization/SKILL.md +240 -0
  218. package/data/skills/bio-methylation-based-detection/SKILL.md +223 -0
  219. package/data/skills/bio-methylation-bismark-alignment/SKILL.md +195 -0
  220. package/data/skills/bio-methylation-calling/SKILL.md +200 -0
  221. package/data/skills/bio-methylation-dmr-detection/SKILL.md +211 -0
  222. package/data/skills/bio-methylation-methylkit/SKILL.md +219 -0
  223. package/data/skills/bio-microbiome-amplicon-processing/SKILL.md +137 -0
  224. package/data/skills/bio-microbiome-differential-abundance/SKILL.md +147 -0
  225. package/data/skills/bio-microbiome-diversity-analysis/SKILL.md +188 -0
  226. package/data/skills/bio-microbiome-functional-prediction/SKILL.md +153 -0
  227. package/data/skills/bio-microbiome-qiime2-workflow/SKILL.md +219 -0
  228. package/data/skills/bio-microbiome-taxonomy-assignment/SKILL.md +168 -0
  229. package/data/skills/bio-molecular-descriptors/SKILL.md +200 -0
  230. package/data/skills/bio-molecular-io/SKILL.md +188 -0
  231. package/data/skills/bio-motif-search/SKILL.md +354 -0
  232. package/data/skills/bio-multi-omics-data-harmonization/SKILL.md +228 -0
  233. package/data/skills/bio-multi-omics-mixomics-analysis/SKILL.md +221 -0
  234. package/data/skills/bio-multi-omics-mofa-integration/SKILL.md +225 -0
  235. package/data/skills/bio-multi-omics-similarity-network/SKILL.md +235 -0
  236. package/data/skills/bio-orchestrator/SKILL.md +133 -0
  237. package/data/skills/bio-paired-end-fastq/SKILL.md +334 -0
  238. package/data/skills/bio-pathway-enrichment-visualization/SKILL.md +278 -0
  239. package/data/skills/bio-pathway-go-enrichment/SKILL.md +218 -0
  240. package/data/skills/bio-pathway-gsea/SKILL.md +227 -0
  241. package/data/skills/bio-pathway-kegg-pathways/SKILL.md +234 -0
  242. package/data/skills/bio-pathway-reactome/SKILL.md +215 -0
  243. package/data/skills/bio-pathway-wikipathways/SKILL.md +255 -0
  244. package/data/skills/bio-pdb-geometric-analysis/SKILL.md +475 -0
  245. package/data/skills/bio-pdb-structure-io/SKILL.md +296 -0
  246. package/data/skills/bio-pdb-structure-modification/SKILL.md +448 -0
  247. package/data/skills/bio-pdb-structure-navigation/SKILL.md +335 -0
  248. package/data/skills/bio-phasing-imputation-genotype-imputation/SKILL.md +201 -0
  249. package/data/skills/bio-phasing-imputation-haplotype-phasing/SKILL.md +190 -0
  250. package/data/skills/bio-phasing-imputation-imputation-qc/SKILL.md +265 -0
  251. package/data/skills/bio-phasing-imputation-reference-panels/SKILL.md +203 -0
  252. package/data/skills/bio-phylo-distance-calculations/SKILL.md +307 -0
  253. package/data/skills/bio-phylo-modern-tree-inference/SKILL.md +274 -0
  254. package/data/skills/bio-phylo-tree-io/SKILL.md +252 -0
  255. package/data/skills/bio-phylo-tree-manipulation/SKILL.md +375 -0
  256. package/data/skills/bio-phylo-tree-visualization/SKILL.md +275 -0
  257. package/data/skills/bio-pileup-generation/SKILL.md +314 -0
  258. package/data/skills/bio-population-genetics-association-testing/SKILL.md +293 -0
  259. package/data/skills/bio-population-genetics-linkage-disequilibrium/SKILL.md +260 -0
  260. package/data/skills/bio-population-genetics-plink-basics/SKILL.md +338 -0
  261. package/data/skills/bio-population-genetics-population-structure/SKILL.md +352 -0
  262. package/data/skills/bio-population-genetics-scikit-allel-analysis/SKILL.md +306 -0
  263. package/data/skills/bio-population-genetics-selection-statistics/SKILL.md +251 -0
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@@ -0,0 +1,271 @@
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+ ---
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+ name: adhd-daily-planner
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+ description: Time-blind friendly planning, executive function support, and daily structure for ADHD brains. Specializes in realistic time estimation, dopamine-aware task design, and building systems that
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+ actually work for neurodivergent minds.
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+ allowed-tools: Read, Edit, Write, Bash, Glob, Grep, WebFetch, WebSearch, Task
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+ metadata:
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+ category: Lifestyle & Personal
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+ pairs-with:
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+ - skill: project-management-guru-adhd
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+ reason: Long-term project planning with ADHD context
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+ - skill: wisdom-accountability-coach
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+ reason: Accountability and habit tracking
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+ tags:
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+ - adhd
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+ - productivity
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+ - planning
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+ - neurodivergent
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+ - executive-function
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+ ---
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+
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+ # ADHD Daily Planner
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+
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+ A planning system designed BY and FOR ADHD brains. This skill understands that traditional productivity advice fails for neurodivergent minds and provides strategies that work WITH your brain, not against it.
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+
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+ ## Core Philosophy
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+
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+ ADHD is not a character flaw or lack of willpower. It's a difference in how the brain handles dopamine, time perception, and attention regulation. This skill:
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+ - Never uses shame or "just try harder" rhetoric
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+ - Builds systems around ADHD realities, not neurotypical ideals
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+ - Acknowledges that what works today might not work tomorrow
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+ - Celebrates done > perfect
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+ - Treats executive function as a battery that depletes
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+
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+ ## The ADHD Planning Paradox
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+
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+ ```
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+ Traditional Planning:
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+ 1. Make detailed plan
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+ 2. Follow plan
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+ 3. Achieve goal
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+
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+ ADHD Reality:
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+ 1. Make detailed plan (hyperfocus, feels great)
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+ 2. Plan feels constraining by day 2
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+ 3. Rebel against own plan
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+ 4. Feel guilty about abandoned plan
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+ 5. Avoid thinking about goal entirely
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+ ```
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+
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+ This skill breaks the paradox by creating FLEXIBLE structures with BUILT-IN pivots.
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+
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+ ## Decision Tree
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+
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+ ```
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+ What time horizon are we planning?
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+ ├── RIGHT NOW (next 2 hours) → Emergency brain dump + single next action
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+ ├── TODAY → Time-blocked structure with transition buffers
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+ ├── THIS WEEK → Theme days + priority winnowing
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+ ├── THIS MONTH → Goal setting with anti-overwhelm safeguards
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+ └── LONGER → Break into month-sized chunks, don't over-plan
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+
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+ Is the person in crisis mode?
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+ ├── YES → Skip planning, identify ONE smallest possible action
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+ └── NO → Proceed with appropriate planning level
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+
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+ Is the person hyperfocusing on planning itself?
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+ ├── YES → Interrupt! Planning ≠ doing. Set timer, start ONE task.
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+ └── NO → Continue planning support
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+ ```
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+
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+ ## Time Blindness Strategies
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+
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+ ### The ADHD Time Estimation Formula
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+
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+ ```
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+ Take your first estimate. Now:
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+
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+ "5 minutes" → Actually 15-20 minutes
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+ "30 minutes" → Actually 1-1.5 hours
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+ "A couple hours" → Actually half a day
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+ "This weekend" → Actually won't happen without body doubling
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+ ```
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+
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+ **The 3x Rule**: Whatever you think it will take, multiply by 3. You're not bad at estimating—your brain processes time differently.
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+
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+ ### Making Time Visible
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+
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+ - **Analog clocks** in every room (digital jumps; analog shows time PASSING)
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+ - **Time Timer** or similar visual countdown timers
90
+ - **Calendar blocking** - if it's not on the calendar with a time, it doesn't exist
91
+ - **"When, then" statements** - "When I finish my coffee, then I start the report"
92
+
93
+ ### Transition Time
94
+
95
+ ADHD brains struggle with task transitions. BUILD IN BUFFERS:
96
+
97
+ ```
98
+ Neurotypical Schedule:
99
+ 9:00 - Meeting
100
+ 10:00 - Deep work
101
+ 12:00 - Lunch
102
+
103
+ ADHD-Friendly Schedule:
104
+ 9:00 - Meeting
105
+ 10:00 - [Transition buffer: bathroom, water, stare at wall]
106
+ 10:15 - Deep work
107
+ 11:45 - [Transition buffer: save work, prepare for context switch]
108
+ 12:00 - Lunch
109
+ ```
110
+
111
+ ## Daily Planning Template
112
+
113
+ ### Morning Brain Dump (5 min max - set timer!)
114
+
115
+ ```
116
+ EVERYTHING IN MY HEAD RIGHT NOW:
117
+ _________________________________
118
+ _________________________________
119
+ _________________________________
120
+ _________________________________
121
+
122
+ NOW CIRCLE ONLY 1-3 THINGS THAT ACTUALLY MATTER TODAY.
123
+ ```
124
+
125
+ ### The "3 Things" System
126
+
127
+ Your daily plan is exactly 3 things:
128
+ 1. **THE Thing** - If you do nothing else, do this
129
+ 2. **Would Be Nice** - Important but not critical today
130
+ 3. **If I'm On Fire** - Only if crushing it
131
+
132
+ That's it. Not 10 things. Not 5 things. THREE.
133
+
134
+ ### Time Blocking for ADHD
135
+
136
+ ```
137
+ ┌─────────────────────────────────────────────────────────────┐
138
+ │ MORNING (Peak brain time for many - protect it!) │
139
+ ├─────────────────────────────────────────────────────────────┤
140
+ │ 9:00 - THE Thing (hardest/most important) │
141
+ │ [Use body doubling, website blockers, timer] │
142
+ │ 10:30 - TRANSITION BUFFER (10-15 min) │
143
+ │ 10:45 - Would Be Nice OR meetings │
144
+ ├─────────────────────────────────────────────────────────────┤
145
+ │ MIDDAY (Energy dip - don't fight it) │
146
+ ├─────────────────────────────────────────────────────────────┤
147
+ │ 12:00 - Lunch (actual break, not working lunch) │
148
+ │ 12:45 - Low-effort tasks: email, admin, organizing │
149
+ ├─────────────────────────────────────────────────────────────┤
150
+ │ AFTERNOON (Second wind for some) │
151
+ ├─────────────────────────────────────────────────────────────┤
152
+ │ 2:00 - Collaborative work, meetings, variety tasks │
153
+ │ 4:00 - Wrap up, tomorrow prep (5 min), shutdown ritual │
154
+ └─────────────────────────────────────────────────────────────┘
155
+ ```
156
+
157
+ ## Executive Function Support
158
+
159
+ ### Task Initiation (The Hardest Part)
160
+
161
+ **The 2-Minute Start**: Don't commit to finishing. Commit to 2 minutes.
162
+ - "I'll just open the document"
163
+ - "I'll just write the first sentence"
164
+ - "I'll just look at the thing"
165
+
166
+ **Body Doubling**: Work alongside someone (physically or virtually). The Focusmate app, Discord study groups, or just a friend on video call.
167
+
168
+ **Temptation Bundling**: Pair unpleasant tasks with pleasant ones.
169
+ - Boring data entry + favorite podcast
170
+ - Exercise + audiobook
171
+ - Cleaning + dance music
172
+
173
+ ### Working Memory Support
174
+
175
+ ADHD working memory is limited. EXTERNALIZE EVERYTHING:
176
+
177
+ - **Capture tools everywhere** - Notes app, physical notepad, voice memos
178
+ - **Written instructions** even for simple things
179
+ - **Checklists** for repeated tasks (even ones you've done 100 times)
180
+ - **Visual reminders** in the physical space where you'll need them
181
+
182
+ ### Decision Fatigue
183
+
184
+ ADHD brains make thousands of micro-decisions that drain the battery:
185
+
186
+ **Pre-decide:**
187
+ - Same breakfast every day (or rotate 2-3 options)
188
+ - Outfit laid out night before
189
+ - Default schedule for types of tasks
190
+ - "If X, then Y" rules that don't require thinking
191
+
192
+ ## The Doom Box Strategy
193
+
194
+ You have doom boxes. Admit it. Those piles of stuff you don't know what to do with.
195
+
196
+ **Weekly Doom Box Protocol (15 min max):**
197
+ 1. Set timer for 15 minutes
198
+ 2. Pick up ONE item from the doom pile
199
+ 3. Decide: Trash / Donate / Home / Action needed
200
+ 4. If Action needed: write the action, put item in "action needed" zone
201
+ 5. Repeat until timer ends
202
+ 6. STOP. You did enough.
203
+
204
+ ## Anti-Patterns (Things That Don't Work)
205
+
206
+ ❌ **Detailed long-term planning** - You'll abandon it and feel bad
207
+ ❌ **Guilt-based motivation** - Creates avoidance, not action
208
+ ❌ **"I'll remember"** - You won't. Write it down.
209
+ ❌ **Willpower over systems** - Systems > willpower every time
210
+ ❌ **Comparing to neurotypical productivity** - Different brain, different metrics
211
+ ❌ **"Catching up" marathons** - You'll burn out. Slow and steady.
212
+ ❌ **Perfect planning before starting** - Planning paralysis. Start messy.
213
+
214
+ ## Good Days vs Bad Days
215
+
216
+ ADHD has high variance. Plan for BOTH:
217
+
218
+ **Good Days (Hyperfocus Available):**
219
+ - Tackle THE Thing first while energy is there
220
+ - Don't overcommit just because you're on fire
221
+ - Bank some wins for bad days
222
+
223
+ **Bad Days (Executive Function Depleted):**
224
+ - Permission to do minimum viable
225
+ - Focus on maintenance (eat, hygiene, rest)
226
+ - Low-stakes tasks only
227
+ - No major decisions
228
+
229
+ **The key**: Don't judge bad days. They're part of the pattern.
230
+
231
+ ## Tools That Actually Help
232
+
233
+ ### Digital
234
+ - **Focusmate** - Body doubling with strangers
235
+ - **Forest** - Phone lockout with gamification
236
+ - **Todoist/Things** - Simple task managers (NOT complex systems)
237
+ - **Goblin Tools** - AI that breaks tasks into smaller steps
238
+
239
+ ### Physical
240
+ - **Time Timer** - Visual countdown
241
+ - **Whiteboard** - Daily view in prominent location
242
+ - **Physical inbox tray** - One place for paper
243
+ - **Fidget tools** - Support focus for many ADHD brains
244
+
245
+ ### Environmental
246
+ - **Background noise** - Lo-fi beats, brown noise, coffee shop sounds
247
+ - **Standing desk or movement option** - Bodies need to move
248
+ - **Minimal visual clutter** - Less distraction
249
+ - **Good lighting** - Affects focus more than you think
250
+
251
+ ## The Shutdown Ritual (5 min)
252
+
253
+ End of workday ritual to actually STOP working:
254
+
255
+ 1. Write tomorrow's "THE Thing" (30 seconds)
256
+ 2. Check calendar for tomorrow surprises (30 seconds)
257
+ 3. Clear one small thing from inbox/desk (2 minutes)
258
+ 4. Say out loud: "Work is done for today." (Seriously. Say it.)
259
+ 5. Physical transition (close laptop, leave room, change clothes)
260
+
261
+ ## Integration with Other Skills
262
+
263
+ - **adhd-design-expert**: For designing ADHD-friendly digital experiences
264
+ - **diagramming-expert**: For visual task mapping
265
+ - **jungian-psychologist**: For deeper patterns around productivity shame
266
+
267
+ ## Remember
268
+
269
+ You are not broken. Your brain works differently. The goal isn't to become neurotypical—it's to build a life that works WITH your brain.
270
+
271
+ Progress over perfection. Compassion over criticism. Systems over willpower.
@@ -0,0 +1,372 @@
1
+ ---
2
+ name: aeon
3
+ description: This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search. Use when working with temporal data, sequential patterns, or time-indexed observations requiring specialized algorithms beyond standard ML approaches. Particularly suited for univariate and multivariate time series analysis with scikit-learn compatible APIs.
4
+ license: BSD-3-Clause license
5
+ metadata:
6
+ skill-author: K-Dense Inc.
7
+ ---
8
+
9
+ # Aeon Time Series Machine Learning
10
+
11
+ ## Overview
12
+
13
+ Aeon is a scikit-learn compatible Python toolkit for time series machine learning. It provides state-of-the-art algorithms for classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search.
14
+
15
+ ## When to Use This Skill
16
+
17
+ Apply this skill when:
18
+ - Classifying or predicting from time series data
19
+ - Detecting anomalies or change points in temporal sequences
20
+ - Clustering similar time series patterns
21
+ - Forecasting future values
22
+ - Finding repeated patterns (motifs) or unusual subsequences (discords)
23
+ - Comparing time series with specialized distance metrics
24
+ - Extracting features from temporal data
25
+
26
+ ## Installation
27
+
28
+ ```bash
29
+ uv pip install aeon
30
+ ```
31
+
32
+ ## Core Capabilities
33
+
34
+ ### 1. Time Series Classification
35
+
36
+ Categorize time series into predefined classes. See `references/classification.md` for complete algorithm catalog.
37
+
38
+ **Quick Start:**
39
+ ```python
40
+ from aeon.classification.convolution_based import RocketClassifier
41
+ from aeon.datasets import load_classification
42
+
43
+ # Load data
44
+ X_train, y_train = load_classification("GunPoint", split="train")
45
+ X_test, y_test = load_classification("GunPoint", split="test")
46
+
47
+ # Train classifier
48
+ clf = RocketClassifier(n_kernels=10000)
49
+ clf.fit(X_train, y_train)
50
+ accuracy = clf.score(X_test, y_test)
51
+ ```
52
+
53
+ **Algorithm Selection:**
54
+ - **Speed + Performance**: `MiniRocketClassifier`, `Arsenal`
55
+ - **Maximum Accuracy**: `HIVECOTEV2`, `InceptionTimeClassifier`
56
+ - **Interpretability**: `ShapeletTransformClassifier`, `Catch22Classifier`
57
+ - **Small Datasets**: `KNeighborsTimeSeriesClassifier` with DTW distance
58
+
59
+ ### 2. Time Series Regression
60
+
61
+ Predict continuous values from time series. See `references/regression.md` for algorithms.
62
+
63
+ **Quick Start:**
64
+ ```python
65
+ from aeon.regression.convolution_based import RocketRegressor
66
+ from aeon.datasets import load_regression
67
+
68
+ X_train, y_train = load_regression("Covid3Month", split="train")
69
+ X_test, y_test = load_regression("Covid3Month", split="test")
70
+
71
+ reg = RocketRegressor()
72
+ reg.fit(X_train, y_train)
73
+ predictions = reg.predict(X_test)
74
+ ```
75
+
76
+ ### 3. Time Series Clustering
77
+
78
+ Group similar time series without labels. See `references/clustering.md` for methods.
79
+
80
+ **Quick Start:**
81
+ ```python
82
+ from aeon.clustering import TimeSeriesKMeans
83
+
84
+ clusterer = TimeSeriesKMeans(
85
+ n_clusters=3,
86
+ distance="dtw",
87
+ averaging_method="ba"
88
+ )
89
+ labels = clusterer.fit_predict(X_train)
90
+ centers = clusterer.cluster_centers_
91
+ ```
92
+
93
+ ### 4. Forecasting
94
+
95
+ Predict future time series values. See `references/forecasting.md` for forecasters.
96
+
97
+ **Quick Start:**
98
+ ```python
99
+ from aeon.forecasting.arima import ARIMA
100
+
101
+ forecaster = ARIMA(order=(1, 1, 1))
102
+ forecaster.fit(y_train)
103
+ y_pred = forecaster.predict(fh=[1, 2, 3, 4, 5])
104
+ ```
105
+
106
+ ### 5. Anomaly Detection
107
+
108
+ Identify unusual patterns or outliers. See `references/anomaly_detection.md` for detectors.
109
+
110
+ **Quick Start:**
111
+ ```python
112
+ from aeon.anomaly_detection import STOMP
113
+
114
+ detector = STOMP(window_size=50)
115
+ anomaly_scores = detector.fit_predict(y)
116
+
117
+ # Higher scores indicate anomalies
118
+ threshold = np.percentile(anomaly_scores, 95)
119
+ anomalies = anomaly_scores > threshold
120
+ ```
121
+
122
+ ### 6. Segmentation
123
+
124
+ Partition time series into regions with change points. See `references/segmentation.md`.
125
+
126
+ **Quick Start:**
127
+ ```python
128
+ from aeon.segmentation import ClaSPSegmenter
129
+
130
+ segmenter = ClaSPSegmenter()
131
+ change_points = segmenter.fit_predict(y)
132
+ ```
133
+
134
+ ### 7. Similarity Search
135
+
136
+ Find similar patterns within or across time series. See `references/similarity_search.md`.
137
+
138
+ **Quick Start:**
139
+ ```python
140
+ from aeon.similarity_search import StompMotif
141
+
142
+ # Find recurring patterns
143
+ motif_finder = StompMotif(window_size=50, k=3)
144
+ motifs = motif_finder.fit_predict(y)
145
+ ```
146
+
147
+ ## Feature Extraction and Transformations
148
+
149
+ Transform time series for feature engineering. See `references/transformations.md`.
150
+
151
+ **ROCKET Features:**
152
+ ```python
153
+ from aeon.transformations.collection.convolution_based import RocketTransformer
154
+
155
+ rocket = RocketTransformer()
156
+ X_features = rocket.fit_transform(X_train)
157
+
158
+ # Use features with any sklearn classifier
159
+ from sklearn.ensemble import RandomForestClassifier
160
+ clf = RandomForestClassifier()
161
+ clf.fit(X_features, y_train)
162
+ ```
163
+
164
+ **Statistical Features:**
165
+ ```python
166
+ from aeon.transformations.collection.feature_based import Catch22
167
+
168
+ catch22 = Catch22()
169
+ X_features = catch22.fit_transform(X_train)
170
+ ```
171
+
172
+ **Preprocessing:**
173
+ ```python
174
+ from aeon.transformations.collection import MinMaxScaler, Normalizer
175
+
176
+ scaler = Normalizer() # Z-normalization
177
+ X_normalized = scaler.fit_transform(X_train)
178
+ ```
179
+
180
+ ## Distance Metrics
181
+
182
+ Specialized temporal distance measures. See `references/distances.md` for complete catalog.
183
+
184
+ **Usage:**
185
+ ```python
186
+ from aeon.distances import dtw_distance, dtw_pairwise_distance
187
+
188
+ # Single distance
189
+ distance = dtw_distance(x, y, window=0.1)
190
+
191
+ # Pairwise distances
192
+ distance_matrix = dtw_pairwise_distance(X_train)
193
+
194
+ # Use with classifiers
195
+ from aeon.classification.distance_based import KNeighborsTimeSeriesClassifier
196
+
197
+ clf = KNeighborsTimeSeriesClassifier(
198
+ n_neighbors=5,
199
+ distance="dtw",
200
+ distance_params={"window": 0.2}
201
+ )
202
+ ```
203
+
204
+ **Available Distances:**
205
+ - **Elastic**: DTW, DDTW, WDTW, ERP, EDR, LCSS, TWE, MSM
206
+ - **Lock-step**: Euclidean, Manhattan, Minkowski
207
+ - **Shape-based**: Shape DTW, SBD
208
+
209
+ ## Deep Learning Networks
210
+
211
+ Neural architectures for time series. See `references/networks.md`.
212
+
213
+ **Architectures:**
214
+ - Convolutional: `FCNClassifier`, `ResNetClassifier`, `InceptionTimeClassifier`
215
+ - Recurrent: `RecurrentNetwork`, `TCNNetwork`
216
+ - Autoencoders: `AEFCNClusterer`, `AEResNetClusterer`
217
+
218
+ **Usage:**
219
+ ```python
220
+ from aeon.classification.deep_learning import InceptionTimeClassifier
221
+
222
+ clf = InceptionTimeClassifier(n_epochs=100, batch_size=32)
223
+ clf.fit(X_train, y_train)
224
+ predictions = clf.predict(X_test)
225
+ ```
226
+
227
+ ## Datasets and Benchmarking
228
+
229
+ Load standard benchmarks and evaluate performance. See `references/datasets_benchmarking.md`.
230
+
231
+ **Load Datasets:**
232
+ ```python
233
+ from aeon.datasets import load_classification, load_regression
234
+
235
+ # Classification
236
+ X_train, y_train = load_classification("ArrowHead", split="train")
237
+
238
+ # Regression
239
+ X_train, y_train = load_regression("Covid3Month", split="train")
240
+ ```
241
+
242
+ **Benchmarking:**
243
+ ```python
244
+ from aeon.benchmarking import get_estimator_results
245
+
246
+ # Compare with published results
247
+ published = get_estimator_results("ROCKET", "GunPoint")
248
+ ```
249
+
250
+ ## Common Workflows
251
+
252
+ ### Classification Pipeline
253
+
254
+ ```python
255
+ from aeon.transformations.collection import Normalizer
256
+ from aeon.classification.convolution_based import RocketClassifier
257
+ from sklearn.pipeline import Pipeline
258
+
259
+ pipeline = Pipeline([
260
+ ('normalize', Normalizer()),
261
+ ('classify', RocketClassifier())
262
+ ])
263
+
264
+ pipeline.fit(X_train, y_train)
265
+ accuracy = pipeline.score(X_test, y_test)
266
+ ```
267
+
268
+ ### Feature Extraction + Traditional ML
269
+
270
+ ```python
271
+ from aeon.transformations.collection import RocketTransformer
272
+ from sklearn.ensemble import GradientBoostingClassifier
273
+
274
+ # Extract features
275
+ rocket = RocketTransformer()
276
+ X_train_features = rocket.fit_transform(X_train)
277
+ X_test_features = rocket.transform(X_test)
278
+
279
+ # Train traditional ML
280
+ clf = GradientBoostingClassifier()
281
+ clf.fit(X_train_features, y_train)
282
+ predictions = clf.predict(X_test_features)
283
+ ```
284
+
285
+ ### Anomaly Detection with Visualization
286
+
287
+ ```python
288
+ from aeon.anomaly_detection import STOMP
289
+ import matplotlib.pyplot as plt
290
+
291
+ detector = STOMP(window_size=50)
292
+ scores = detector.fit_predict(y)
293
+
294
+ plt.figure(figsize=(15, 5))
295
+ plt.subplot(2, 1, 1)
296
+ plt.plot(y, label='Time Series')
297
+ plt.subplot(2, 1, 2)
298
+ plt.plot(scores, label='Anomaly Scores', color='red')
299
+ plt.axhline(np.percentile(scores, 95), color='k', linestyle='--')
300
+ plt.show()
301
+ ```
302
+
303
+ ## Best Practices
304
+
305
+ ### Data Preparation
306
+
307
+ 1. **Normalize**: Most algorithms benefit from z-normalization
308
+ ```python
309
+ from aeon.transformations.collection import Normalizer
310
+ normalizer = Normalizer()
311
+ X_train = normalizer.fit_transform(X_train)
312
+ X_test = normalizer.transform(X_test)
313
+ ```
314
+
315
+ 2. **Handle Missing Values**: Impute before analysis
316
+ ```python
317
+ from aeon.transformations.collection import SimpleImputer
318
+ imputer = SimpleImputer(strategy='mean')
319
+ X_train = imputer.fit_transform(X_train)
320
+ ```
321
+
322
+ 3. **Check Data Format**: Aeon expects shape `(n_samples, n_channels, n_timepoints)`
323
+
324
+ ### Model Selection
325
+
326
+ 1. **Start Simple**: Begin with ROCKET variants before deep learning
327
+ 2. **Use Validation**: Split training data for hyperparameter tuning
328
+ 3. **Compare Baselines**: Test against simple methods (1-NN Euclidean, Naive)
329
+ 4. **Consider Resources**: ROCKET for speed, deep learning if GPU available
330
+
331
+ ### Algorithm Selection Guide
332
+
333
+ **For Fast Prototyping:**
334
+ - Classification: `MiniRocketClassifier`
335
+ - Regression: `MiniRocketRegressor`
336
+ - Clustering: `TimeSeriesKMeans` with Euclidean
337
+
338
+ **For Maximum Accuracy:**
339
+ - Classification: `HIVECOTEV2`, `InceptionTimeClassifier`
340
+ - Regression: `InceptionTimeRegressor`
341
+ - Forecasting: `ARIMA`, `TCNForecaster`
342
+
343
+ **For Interpretability:**
344
+ - Classification: `ShapeletTransformClassifier`, `Catch22Classifier`
345
+ - Features: `Catch22`, `TSFresh`
346
+
347
+ **For Small Datasets:**
348
+ - Distance-based: `KNeighborsTimeSeriesClassifier` with DTW
349
+ - Avoid: Deep learning (requires large data)
350
+
351
+ ## Reference Documentation
352
+
353
+ Detailed information available in `references/`:
354
+ - `classification.md` - All classification algorithms
355
+ - `regression.md` - Regression methods
356
+ - `clustering.md` - Clustering algorithms
357
+ - `forecasting.md` - Forecasting approaches
358
+ - `anomaly_detection.md` - Anomaly detection methods
359
+ - `segmentation.md` - Segmentation algorithms
360
+ - `similarity_search.md` - Pattern matching and motif discovery
361
+ - `transformations.md` - Feature extraction and preprocessing
362
+ - `distances.md` - Time series distance metrics
363
+ - `networks.md` - Deep learning architectures
364
+ - `datasets_benchmarking.md` - Data loading and evaluation tools
365
+
366
+ ## Additional Resources
367
+
368
+ - Documentation: https://www.aeon-toolkit.org/
369
+ - GitHub: https://github.com/aeon-toolkit/aeon
370
+ - Examples: https://www.aeon-toolkit.org/en/stable/examples.html
371
+ - API Reference: https://www.aeon-toolkit.org/en/stable/api_reference.html
372
+