encode-toolkit 0.3.0b1__tar.gz → 0.3.0b2__tar.gz

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 (282) hide show
  1. encode_toolkit-0.3.0b2/.claude-plugin/marketplace.json +13 -0
  2. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/.claude-plugin/plugin.json +1 -1
  3. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/.github/workflows/release.yml +13 -1
  4. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/PKG-INFO +1 -1
  5. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/package.json +1 -1
  6. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/pyproject.toml +1 -1
  7. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/.claude/settings.json +0 -0
  8. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/.env.example +0 -0
  9. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/.github/ISSUE_TEMPLATE/bug_report.yml +0 -0
  10. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/.github/ISSUE_TEMPLATE/feature_request.yml +0 -0
  11. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/.github/PULL_REQUEST_TEMPLATE.md +0 -0
  12. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/.github/dependabot.yml +0 -0
  13. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/.github/workflows/lint.yml +0 -0
  14. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/.github/workflows/test.yml +0 -0
  15. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/.github/workflows/validate.yml +0 -0
  16. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/.gitignore +0 -0
  17. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/.mcp.json +0 -0
  18. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/.pre-commit-config.yaml +0 -0
  19. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/CHANGELOG.md +0 -0
  20. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/CLAUDE.md +0 -0
  21. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/CONTRIBUTING.md +0 -0
  22. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/Dockerfile +0 -0
  23. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/LICENSE +0 -0
  24. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/PRIVACY.md +0 -0
  25. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/README.md +0 -0
  26. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/SECURITY.md +0 -0
  27. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/conftest.py +0 -0
  28. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/SHOWCASE.md +0 -0
  29. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/api-reference.md +0 -0
  30. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/icon.svg +0 -0
  31. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/integrations.md +0 -0
  32. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/security.md +0 -0
  33. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/accessibility-aggregation.md +0 -0
  34. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/batch-analysis.md +0 -0
  35. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/cellxgene-context.md +0 -0
  36. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/cite-encode.md +0 -0
  37. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/clinvar-annotation.md +0 -0
  38. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/compare-biosamples.md +0 -0
  39. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/cross-reference.md +0 -0
  40. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/data-provenance.md +0 -0
  41. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/disease-research.md +0 -0
  42. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/download-encode.md +0 -0
  43. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/ensembl-annotation.md +0 -0
  44. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/epigenome-profiling.md +0 -0
  45. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/geo-connector.md +0 -0
  46. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/gnomad-variants.md +0 -0
  47. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/gtex-expression.md +0 -0
  48. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/gwas-catalog.md +0 -0
  49. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/hic-aggregation.md +0 -0
  50. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/histone-aggregation.md +0 -0
  51. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/integrative-analysis.md +0 -0
  52. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/jaspar-motifs.md +0 -0
  53. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/methylation-aggregation.md +0 -0
  54. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/motif-analysis.md +0 -0
  55. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/multi-omics-integration.md +0 -0
  56. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/peak-annotation.md +0 -0
  57. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/pipeline-atacseq.md +0 -0
  58. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/pipeline-chipseq.md +0 -0
  59. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/pipeline-cutandrun.md +0 -0
  60. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/pipeline-dnaseseq.md +0 -0
  61. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/pipeline-guide.md +0 -0
  62. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/pipeline-hic.md +0 -0
  63. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/pipeline-rnaseq.md +0 -0
  64. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/pipeline-wgbs.md +0 -0
  65. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/publication-trust.md +0 -0
  66. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/quality-assessment.md +0 -0
  67. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/regulatory-elements.md +0 -0
  68. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/scrna-meta-analysis.md +0 -0
  69. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/search-encode.md +0 -0
  70. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/setup.md +0 -0
  71. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/single-cell-encode.md +0 -0
  72. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/track-experiments.md +0 -0
  73. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/ucsc-browser.md +0 -0
  74. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/variant-annotation.md +0 -0
  75. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/skill-vignettes/visualization-workflow.md +0 -0
  76. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/submission-examples.md +0 -0
  77. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/vignettes/01-discovery-and-search.md +0 -0
  78. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/vignettes/02-download-and-track.md +0 -0
  79. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/vignettes/03-epigenomics-workflow.md +0 -0
  80. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/vignettes/04-variant-and-disease.md +0 -0
  81. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/vignettes/05-expression-and-single-cell.md +0 -0
  82. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/vignettes/06-motif-and-regulatory.md +0 -0
  83. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/vignettes/07-3d-genome-and-methylation.md +0 -0
  84. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/vignettes/08-pipeline-execution.md +0 -0
  85. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/vignettes/09-cross-reference-and-integration.md +0 -0
  86. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/vignettes/_captured_output.md +0 -0
  87. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/docs/walkthrough.md +0 -0
  88. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/index.js +0 -0
  89. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/server.json +0 -0
  90. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/accessibility-aggregation/SKILL.md +0 -0
  91. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/accessibility-aggregation/references/atac-vs-dnase.md +0 -0
  92. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/accessibility-aggregation/references/literature.md +0 -0
  93. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/accessibility-aggregation/scripts/validate_peaks.py +0 -0
  94. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/batch-analysis/SKILL.md +0 -0
  95. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/batch-analysis/references/literature.md +0 -0
  96. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/bioinformatics-installer/SKILL.md +0 -0
  97. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/bioinformatics-installer/environments/atacseq-env.yml +0 -0
  98. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/bioinformatics-installer/environments/chipseq-env.yml +0 -0
  99. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/bioinformatics-installer/environments/cutandrun-env.yml +0 -0
  100. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/bioinformatics-installer/environments/dnaseseq-env.yml +0 -0
  101. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/bioinformatics-installer/environments/hic-env.yml +0 -0
  102. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/bioinformatics-installer/environments/rnaseq-env.yml +0 -0
  103. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/bioinformatics-installer/environments/wgbs-env.yml +0 -0
  104. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/bioinformatics-installer/references/literature.md +0 -0
  105. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/bioinformatics-installer/scripts/install-nextflow.sh +0 -0
  106. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/bioinformatics-installer/scripts/install-python-packages.sh +0 -0
  107. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/bioinformatics-installer/scripts/install-r-packages.R +0 -0
  108. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/cellxgene-context/SKILL.md +0 -0
  109. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/cellxgene-context/references/literature.md +0 -0
  110. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/cite-encode/SKILL.md +0 -0
  111. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/cite-encode/references/literature.md +0 -0
  112. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/clinvar-annotation/SKILL.md +0 -0
  113. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/clinvar-annotation/references/literature.md +0 -0
  114. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/compare-biosamples/SKILL.md +0 -0
  115. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/compare-biosamples/references/literature.md +0 -0
  116. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/cross-reference/SKILL.md +0 -0
  117. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/cross-reference/references/literature.md +0 -0
  118. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/data-provenance/SKILL.md +0 -0
  119. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/data-provenance/references/literature.md +0 -0
  120. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/disease-research/SKILL.md +0 -0
  121. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/disease-research/references/literature.md +0 -0
  122. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/download-encode/SKILL.md +0 -0
  123. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/download-encode/references/literature.md +0 -0
  124. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/ensembl-annotation/SKILL.md +0 -0
  125. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/ensembl-annotation/references/literature.md +0 -0
  126. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/epigenome-profiling/SKILL.md +0 -0
  127. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/epigenome-profiling/references/literature.md +0 -0
  128. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/functional-screen-analysis/SKILL.md +0 -0
  129. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/functional-screen-analysis/references/literature.md +0 -0
  130. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/geo-connector/SKILL.md +0 -0
  131. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/geo-connector/references/literature.md +0 -0
  132. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/gnomad-variants/SKILL.md +0 -0
  133. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/gnomad-variants/references/literature.md +0 -0
  134. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/gtex-expression/SKILL.md +0 -0
  135. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/gtex-expression/references/literature.md +0 -0
  136. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/gwas-catalog/SKILL.md +0 -0
  137. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/gwas-catalog/references/literature.md +0 -0
  138. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/hic-aggregation/SKILL.md +0 -0
  139. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/hic-aggregation/references/literature.md +0 -0
  140. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/hic-aggregation/references/loop-caller-comparison.md +0 -0
  141. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/hic-aggregation/scripts/validate_loops.py +0 -0
  142. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/histone-aggregation/SKILL.md +0 -0
  143. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/histone-aggregation/references/broad-vs-narrow.md +0 -0
  144. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/histone-aggregation/references/histone-marks-reference.md +0 -0
  145. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/histone-aggregation/references/literature.md +0 -0
  146. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/histone-aggregation/references/signal-filtering.md +0 -0
  147. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/histone-aggregation/scripts/validate_peaks.py +0 -0
  148. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/integrative-analysis/SKILL.md +0 -0
  149. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/integrative-analysis/references/literature.md +0 -0
  150. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/jaspar-motifs/SKILL.md +0 -0
  151. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/jaspar-motifs/references/literature.md +0 -0
  152. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/liftover-coordinates/SKILL.md +0 -0
  153. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/liftover-coordinates/references/literature.md +0 -0
  154. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/methylation-aggregation/SKILL.md +0 -0
  155. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/methylation-aggregation/references/hmr-definitions.md +0 -0
  156. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/methylation-aggregation/references/literature.md +0 -0
  157. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/methylation-aggregation/scripts/validate_methylation.py +0 -0
  158. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/motif-analysis/SKILL.md +0 -0
  159. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/motif-analysis/references/literature.md +0 -0
  160. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/multi-omics-integration/SKILL.md +0 -0
  161. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/multi-omics-integration/references/literature.md +0 -0
  162. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/peak-annotation/SKILL.md +0 -0
  163. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/peak-annotation/references/literature.md +0 -0
  164. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-atacseq/SKILL.md +0 -0
  165. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-atacseq/references/01-qc-trimming.md +0 -0
  166. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-atacseq/references/02-alignment.md +0 -0
  167. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-atacseq/references/03-tn5-filtering.md +0 -0
  168. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-atacseq/references/04-peak-calling.md +0 -0
  169. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-atacseq/references/05-qc-metrics.md +0 -0
  170. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-atacseq/references/literature.md +0 -0
  171. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-atacseq/scripts/Dockerfile +0 -0
  172. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-atacseq/scripts/main.nf +0 -0
  173. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-atacseq/scripts/nextflow.config +0 -0
  174. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-chipseq/SKILL.md +0 -0
  175. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-chipseq/references/01-qc-trimming.md +0 -0
  176. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-chipseq/references/02-alignment.md +0 -0
  177. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-chipseq/references/03-filtering.md +0 -0
  178. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-chipseq/references/04-analysis.md +0 -0
  179. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-chipseq/references/05-qc-metrics.md +0 -0
  180. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-chipseq/references/literature.md +0 -0
  181. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-chipseq/scripts/Dockerfile +0 -0
  182. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-chipseq/scripts/main.nf +0 -0
  183. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-chipseq/scripts/nextflow.config +0 -0
  184. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-cutandrun/SKILL.md +0 -0
  185. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-cutandrun/references/01-qc-trimming.md +0 -0
  186. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-cutandrun/references/02-bowtie2-alignment.md +0 -0
  187. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-cutandrun/references/03-filtering-spikein.md +0 -0
  188. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-cutandrun/references/04-seacr-peaks.md +0 -0
  189. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-cutandrun/references/05-qc-metrics.md +0 -0
  190. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-cutandrun/references/literature.md +0 -0
  191. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-cutandrun/scripts/Dockerfile +0 -0
  192. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-cutandrun/scripts/main.nf +0 -0
  193. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-cutandrun/scripts/nextflow.config +0 -0
  194. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-dnaseseq/SKILL.md +0 -0
  195. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-dnaseseq/references/01-qc-trimming.md +0 -0
  196. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-dnaseseq/references/02-alignment.md +0 -0
  197. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-dnaseseq/references/03-filtering.md +0 -0
  198. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-dnaseseq/references/04-hotspot-calling.md +0 -0
  199. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-dnaseseq/references/05-footprinting.md +0 -0
  200. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-dnaseseq/references/literature.md +0 -0
  201. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-dnaseseq/scripts/Dockerfile +0 -0
  202. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-dnaseseq/scripts/main.nf +0 -0
  203. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-dnaseseq/scripts/nextflow.config +0 -0
  204. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-guide/SKILL.md +0 -0
  205. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-guide/references/literature.md +0 -0
  206. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-hic/SKILL.md +0 -0
  207. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-hic/references/01-qc-trimming.md +0 -0
  208. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-hic/references/02-alignment.md +0 -0
  209. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-hic/references/03-pair-processing.md +0 -0
  210. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-hic/references/04-matrix-generation.md +0 -0
  211. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-hic/references/05-loop-calling.md +0 -0
  212. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-hic/references/literature.md +0 -0
  213. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-hic/scripts/Dockerfile +0 -0
  214. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-hic/scripts/main.nf +0 -0
  215. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-hic/scripts/nextflow.config +0 -0
  216. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-rnaseq/SKILL.md +0 -0
  217. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-rnaseq/references/01-qc-trimming.md +0 -0
  218. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-rnaseq/references/02-star-alignment.md +0 -0
  219. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-rnaseq/references/03-quantification.md +0 -0
  220. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-rnaseq/references/04-signal-tracks.md +0 -0
  221. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-rnaseq/references/05-qc-metrics.md +0 -0
  222. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-rnaseq/references/literature.md +0 -0
  223. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-rnaseq/scripts/Dockerfile +0 -0
  224. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-rnaseq/scripts/main.nf +0 -0
  225. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-rnaseq/scripts/nextflow.config +0 -0
  226. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-wgbs/SKILL.md +0 -0
  227. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-wgbs/references/01-qc-trimming.md +0 -0
  228. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-wgbs/references/02-bismark-alignment.md +0 -0
  229. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-wgbs/references/03-dedup-filtering.md +0 -0
  230. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-wgbs/references/04-methylation-calling.md +0 -0
  231. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-wgbs/references/05-qc-metrics.md +0 -0
  232. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-wgbs/references/literature.md +0 -0
  233. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-wgbs/scripts/Dockerfile +0 -0
  234. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-wgbs/scripts/main.nf +0 -0
  235. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/pipeline-wgbs/scripts/nextflow.config +0 -0
  236. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/publication-trust/SKILL.md +0 -0
  237. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/publication-trust/references/literature.md +0 -0
  238. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/quality-assessment/SKILL.md +0 -0
  239. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/quality-assessment/references/literature.md +0 -0
  240. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/regulatory-elements/SKILL.md +0 -0
  241. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/regulatory-elements/references/literature.md +0 -0
  242. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/scientific-writing/SKILL.md +0 -0
  243. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/scientific-writing/references/literature.md +0 -0
  244. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/scrna-meta-analysis/SKILL.md +0 -0
  245. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/scrna-meta-analysis/references/literature.md +0 -0
  246. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/search-encode/SKILL.md +0 -0
  247. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/search-encode/references/literature.md +0 -0
  248. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/setup/SKILL.md +0 -0
  249. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/setup/references/literature.md +0 -0
  250. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/single-cell-encode/SKILL.md +0 -0
  251. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/single-cell-encode/references/literature.md +0 -0
  252. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/track-experiments/SKILL.md +0 -0
  253. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/track-experiments/references/literature.md +0 -0
  254. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/ucsc-browser/SKILL.md +0 -0
  255. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/ucsc-browser/references/literature.md +0 -0
  256. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/variant-annotation/SKILL.md +0 -0
  257. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/variant-annotation/references/literature.md +0 -0
  258. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/visualization-workflow/SKILL.md +0 -0
  259. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/skills/visualization-workflow/references/literature.md +0 -0
  260. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/smithery.yaml +0 -0
  261. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/src/encode_connector/__init__.py +0 -0
  262. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/src/encode_connector/__main__.py +0 -0
  263. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/src/encode_connector/client/__init__.py +0 -0
  264. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/src/encode_connector/client/auth.py +0 -0
  265. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/src/encode_connector/client/constants.py +0 -0
  266. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/src/encode_connector/client/downloader.py +0 -0
  267. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/src/encode_connector/client/encode_client.py +0 -0
  268. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/src/encode_connector/client/models.py +0 -0
  269. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/src/encode_connector/client/tracker.py +0 -0
  270. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/src/encode_connector/client/validation.py +0 -0
  271. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/src/encode_connector/server/__init__.py +0 -0
  272. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/src/encode_connector/server/__main__.py +0 -0
  273. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/src/encode_connector/server/main.py +0 -0
  274. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/tests/__init__.py +0 -0
  275. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/tests/test_auth.py +0 -0
  276. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/tests/test_client.py +0 -0
  277. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/tests/test_downloader.py +0 -0
  278. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/tests/test_models.py +0 -0
  279. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/tests/test_server.py +0 -0
  280. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/tests/test_tool_responses.py +0 -0
  281. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/tests/test_tracker.py +0 -0
  282. {encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/tests/test_validation.py +0 -0
encode_toolkit-0.3.0b2/.claude-plugin/marketplace.json ADDED
@@ -0,0 +1,13 @@
1
+ {
2
+ "name": "encode-toolkit",
3
+ "owner": {
4
+ "name": "Dr. Alex M. Mawla, PhD"
5
+ },
6
+ "plugins": [
7
+ {
8
+ "name": "encode-toolkit",
9
+ "source": ".",
10
+ "description": "20 ENCODE API tools + 48 expert skills for genomics research. Search experiments, download files with MD5 verification, run pipelines, and cross-reference 14 databases."
11
+ }
12
+ ]
13
+ }
{encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/.claude-plugin/plugin.json RENAMED
@@ -1,7 +1,7 @@
1
1
  {
2
2
  "name": "encode-toolkit",
3
3
  "description": "20 ENCODE API tools + 48 expert skills for genomics research. Search experiments, download files with MD5 verification, run pipelines, and cross-reference 14 databases.",
4
- "version": "0.3.0-beta.1",
4
+ "version": "0.3.0-beta.2",
5
5
  "author": {
6
6
  "name": "Dr. Alex M. Mawla, PhD",
7
7
  "email": "ammawla@ucdavis.edu"
{encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/.github/workflows/release.yml RENAMED
@@ -113,7 +113,19 @@ jobs:
113
113
  node-version: "20"
114
114
  registry-url: "https://registry.npmjs.org"
115
115
 
116
+ - name: Determine npm tag
117
+ id: npm-tag
118
+ run: |
119
+ TAG_NAME="${GITHUB_REF#refs/tags/}"
120
+ if echo "$TAG_NAME" | grep -qE 'beta|rc|alpha'; then
121
+ echo "tag=beta" >> "$GITHUB_OUTPUT"
122
+ else
123
+ echo "tag=latest" >> "$GITHUB_OUTPUT"
124
+ fi
125
+ env:
126
+ GITHUB_REF: ${{ github.ref }}
127
+
116
128
  - name: Publish to npm
117
- run: npm publish --access public
129
+ run: npm publish --access public --tag ${{ steps.npm-tag.outputs.tag }}
118
130
  env:
119
131
  NODE_AUTH_TOKEN: ${{ secrets.NPM_TOKEN }}
{encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: encode-toolkit
3
- Version: 0.3.0b1
3
+ Version: 0.3.0b2
4
4
  Summary: MCP server for querying and downloading ENCODE Project genomics data directly from Claude
5
5
  Project-URL: Homepage, https://github.com/ammawla/encode-toolkit
6
6
  Project-URL: Repository, https://github.com/ammawla/encode-toolkit
{encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/package.json RENAMED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "encode-toolkit",
3
- "version": "0.3.0-beta.1",
3
+ "version": "0.3.0-beta.2",
4
4
  "description": "ENCODE Toolkit — Genomics research infrastructure with 20 MCP tools, 47 skills, 14 database integrations, and 7 pipelines for Claude Code",
5
5
  "main": "index.js",
6
6
  "bin": {
{encode_toolkit-0.3.0b1 → encode_toolkit-0.3.0b2}/pyproject.toml RENAMED
@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
4
4
 
5
5
  [project]
6
6
  name = "encode-toolkit"
7
- version = "0.3.0b1"
7
+ version = "0.3.0b2"
8
8
  description = "MCP server for querying and downloading ENCODE Project genomics data directly from Claude"
9
9
  readme = "README.md"
10
10
  license = "LicenseRef-Noncommercial"