@bgicli/bgicli 2.4.6 → 2.4.8

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 (356) hide show
  1. package/dist/bgi.js +82 -28
  2. package/package.json +1 -1
  3. /package/data/{workflows → skills}/bulk-omics-clustering/SKILL.md +0 -0
  4. /package/data/{workflows → skills}/bulk-omics-clustering/references/best_practices.md +0 -0
  5. /package/data/{workflows → skills}/bulk-omics-clustering/references/clustering_methods_comparison.md +0 -0
  6. /package/data/{workflows → skills}/bulk-omics-clustering/references/common-patterns.md +0 -0
  7. /package/data/{workflows → skills}/bulk-omics-clustering/references/decision-guide.md +0 -0
  8. /package/data/{workflows → skills}/bulk-omics-clustering/references/distance_metrics_guide.md +0 -0
  9. /package/data/{workflows → skills}/bulk-omics-clustering/references/parameter_guide.md +0 -0
  10. /package/data/{workflows → skills}/bulk-omics-clustering/references/r-quick-start.md +0 -0
  11. /package/data/{workflows → skills}/bulk-omics-clustering/references/validation_metrics_guide.md +0 -0
  12. /package/data/{workflows → skills}/bulk-omics-clustering/scripts/characterize_clusters.py +0 -0
  13. /package/data/{workflows → skills}/bulk-omics-clustering/scripts/cluster_validation.py +0 -0
  14. /package/data/{workflows → skills}/bulk-omics-clustering/scripts/density_clustering.py +0 -0
  15. /package/data/{workflows → skills}/bulk-omics-clustering/scripts/dimensionality_reduction.py +0 -0
  16. /package/data/{workflows → skills}/bulk-omics-clustering/scripts/distance_metrics.py +0 -0
  17. /package/data/{workflows → skills}/bulk-omics-clustering/scripts/export_results.py +0 -0
  18. /package/data/{workflows → skills}/bulk-omics-clustering/scripts/hierarchical_clustering.R +0 -0
  19. /package/data/{workflows → skills}/bulk-omics-clustering/scripts/hierarchical_clustering.py +0 -0
  20. /package/data/{workflows → skills}/bulk-omics-clustering/scripts/kmeans_clustering.py +0 -0
  21. /package/data/{workflows → skills}/bulk-omics-clustering/scripts/load_example_data.R +0 -0
  22. /package/data/{workflows → skills}/bulk-omics-clustering/scripts/load_example_data.py +0 -0
  23. /package/data/{workflows → skills}/bulk-omics-clustering/scripts/model_based_clustering.py +0 -0
  24. /package/data/{workflows → skills}/bulk-omics-clustering/scripts/optimal_clusters.py +0 -0
  25. /package/data/{workflows → skills}/bulk-omics-clustering/scripts/plot_cluster_heatmap.R +0 -0
  26. /package/data/{workflows → skills}/bulk-omics-clustering/scripts/plot_clustering_results.py +0 -0
  27. /package/data/{workflows → skills}/bulk-omics-clustering/scripts/prepare_data.py +0 -0
  28. /package/data/{workflows → skills}/bulk-omics-clustering/scripts/stability_analysis.py +0 -0
  29. /package/data/{workflows → skills}/bulk-rnaseq-counts-to-de-deseq2/SKILL.md +0 -0
  30. /package/data/{workflows → skills}/bulk-rnaseq-counts-to-de-deseq2/references/comprehensive-reference.md +0 -0
  31. /package/data/{workflows → skills}/bulk-rnaseq-counts-to-de-deseq2/references/decision-guide.md +0 -0
  32. /package/data/{workflows → skills}/bulk-rnaseq-counts-to-de-deseq2/references/troubleshooting.md +0 -0
  33. /package/data/{workflows → skills}/bulk-rnaseq-counts-to-de-deseq2/references/usage-guide.md +0 -0
  34. /package/data/{workflows → skills}/bulk-rnaseq-counts-to-de-deseq2/scripts/basic_workflow.R +0 -0
  35. /package/data/{workflows → skills}/bulk-rnaseq-counts-to-de-deseq2/scripts/batch_correction.R +0 -0
  36. /package/data/{workflows → skills}/bulk-rnaseq-counts-to-de-deseq2/scripts/export_results.R +0 -0
  37. /package/data/{workflows → skills}/bulk-rnaseq-counts-to-de-deseq2/scripts/extract_results.R +0 -0
  38. /package/data/{workflows → skills}/bulk-rnaseq-counts-to-de-deseq2/scripts/load_example_data.R +0 -0
  39. /package/data/{workflows → skills}/bulk-rnaseq-counts-to-de-deseq2/scripts/multi_condition.R +0 -0
  40. /package/data/{workflows → skills}/bulk-rnaseq-counts-to-de-deseq2/scripts/qc_plots.R +0 -0
  41. /package/data/{workflows → skills}/bulk-rnaseq-counts-to-de-deseq2/scripts/transformations.R +0 -0
  42. /package/data/{workflows → skills}/chip-atlas-diff-analysis/SKILL.md +0 -0
  43. /package/data/{workflows → skills}/chip-atlas-diff-analysis/references/chipatlas_diff_api_format.md +0 -0
  44. /package/data/{workflows → skills}/chip-atlas-diff-analysis/references/diff_analysis_methods.md +0 -0
  45. /package/data/{workflows → skills}/chip-atlas-diff-analysis/references/output_format.md +0 -0
  46. /package/data/{workflows → skills}/chip-atlas-diff-analysis/scripts/__init__.py +0 -0
  47. /package/data/{workflows → skills}/chip-atlas-diff-analysis/scripts/annotate_genes.py +0 -0
  48. /package/data/{workflows → skills}/chip-atlas-diff-analysis/scripts/export_all.py +0 -0
  49. /package/data/{workflows → skills}/chip-atlas-diff-analysis/scripts/filter_regions.py +0 -0
  50. /package/data/{workflows → skills}/chip-atlas-diff-analysis/scripts/generate_all_plots.py +0 -0
  51. /package/data/{workflows → skills}/chip-atlas-diff-analysis/scripts/load_example_data.py +0 -0
  52. /package/data/{workflows → skills}/chip-atlas-diff-analysis/scripts/load_user_data.py +0 -0
  53. /package/data/{workflows → skills}/chip-atlas-diff-analysis/scripts/parse_bed_results.py +0 -0
  54. /package/data/{workflows → skills}/chip-atlas-diff-analysis/scripts/qc_checks.py +0 -0
  55. /package/data/{workflows → skills}/chip-atlas-diff-analysis/scripts/query_chipatlas_api.py +0 -0
  56. /package/data/{workflows → skills}/chip-atlas-diff-analysis/scripts/run_diff_workflow.py +0 -0
  57. /package/data/{workflows → skills}/chip-atlas-peak-enrichment/SKILL.md +0 -0
  58. /package/data/{workflows → skills}/chip-atlas-peak-enrichment/references/chipatlas_metadata_format.md +0 -0
  59. /package/data/{workflows → skills}/chip-atlas-peak-enrichment/references/enrichment_statistics.md +0 -0
  60. /package/data/{workflows → skills}/chip-atlas-peak-enrichment/references/peak_thresholds.md +0 -0
  61. /package/data/{workflows → skills}/chip-atlas-peak-enrichment/references/promoter_definitions.md +0 -0
  62. /package/data/{workflows → skills}/chip-atlas-peak-enrichment/scripts/__init__.py +0 -0
  63. /package/data/{workflows → skills}/chip-atlas-peak-enrichment/scripts/convert_genes_to_regions.py +0 -0
  64. /package/data/{workflows → skills}/chip-atlas-peak-enrichment/scripts/export_all.py +0 -0
  65. /package/data/{workflows → skills}/chip-atlas-peak-enrichment/scripts/filter_experiments.py +0 -0
  66. /package/data/{workflows → skills}/chip-atlas-peak-enrichment/scripts/generate_all_plots.py +0 -0
  67. /package/data/{workflows → skills}/chip-atlas-peak-enrichment/scripts/load_example_data.py +0 -0
  68. /package/data/{workflows → skills}/chip-atlas-peak-enrichment/scripts/load_user_data.py +0 -0
  69. /package/data/{workflows → skills}/chip-atlas-peak-enrichment/scripts/query_chipatlas_api.py +0 -0
  70. /package/data/{workflows → skills}/chip-atlas-peak-enrichment/scripts/run_enrichment_workflow.py +0 -0
  71. /package/data/{workflows → skills}/chip-atlas-target-genes/SKILL.md +0 -0
  72. /package/data/{workflows → skills}/chip-atlas-target-genes/references/macs2_binding_scores.md +0 -0
  73. /package/data/{workflows → skills}/chip-atlas-target-genes/references/string_scores.md +0 -0
  74. /package/data/{workflows → skills}/chip-atlas-target-genes/references/target_genes_data_format.md +0 -0
  75. /package/data/{workflows → skills}/chip-atlas-target-genes/scripts/__init__.py +0 -0
  76. /package/data/{workflows → skills}/chip-atlas-target-genes/scripts/download_target_genes.py +0 -0
  77. /package/data/{workflows → skills}/chip-atlas-target-genes/scripts/export_all.py +0 -0
  78. /package/data/{workflows → skills}/chip-atlas-target-genes/scripts/filter_targets.py +0 -0
  79. /package/data/{workflows → skills}/chip-atlas-target-genes/scripts/generate_all_plots.py +0 -0
  80. /package/data/{workflows → skills}/chip-atlas-target-genes/scripts/load_example_query.py +0 -0
  81. /package/data/{workflows → skills}/chip-atlas-target-genes/scripts/load_user_query.py +0 -0
  82. /package/data/{workflows → skills}/chip-atlas-target-genes/scripts/run_target_genes_workflow.py +0 -0
  83. /package/data/{workflows → skills}/clinicaltrials-landscape/SKILL.md +0 -0
  84. /package/data/{workflows → skills}/clinicaltrials-landscape/references/api-parameters.md +0 -0
  85. /package/data/{workflows → skills}/clinicaltrials-landscape/references/mechanisms.md +0 -0
  86. /package/data/{workflows → skills}/clinicaltrials-landscape/references/output-schema.md +0 -0
  87. /package/data/{workflows → skills}/clinicaltrials-landscape/scripts/__init__.py +0 -0
  88. /package/data/{workflows → skills}/clinicaltrials-landscape/scripts/classify_mechanisms.py +0 -0
  89. /package/data/{workflows → skills}/clinicaltrials-landscape/scripts/compile_trials.py +0 -0
  90. /package/data/{workflows → skills}/clinicaltrials-landscape/scripts/disease_config.py +0 -0
  91. /package/data/{workflows → skills}/clinicaltrials-landscape/scripts/export_all.py +0 -0
  92. /package/data/{workflows → skills}/clinicaltrials-landscape/scripts/generate_landscape_plots.py +0 -0
  93. /package/data/{workflows → skills}/clinicaltrials-landscape/scripts/generate_pdf_report.py +0 -0
  94. /package/data/{workflows → skills}/clinicaltrials-landscape/scripts/generate_report.py +0 -0
  95. /package/data/{workflows → skills}/clinicaltrials-landscape/scripts/query_clinicaltrials.py +0 -0
  96. /package/data/{workflows → skills}/coexpression-network/SKILL.md +0 -0
  97. /package/data/{workflows → skills}/coexpression-network/references/parameter-tuning-guide.md +0 -0
  98. /package/data/{workflows → skills}/coexpression-network/references/troubleshooting.md +0 -0
  99. /package/data/{workflows → skills}/coexpression-network/references/wgcna-best-practices.md +0 -0
  100. /package/data/{workflows → skills}/coexpression-network/references/wgcna-reference.md +0 -0
  101. /package/data/{workflows → skills}/coexpression-network/scripts/build_network.R +0 -0
  102. /package/data/{workflows → skills}/coexpression-network/scripts/correlate_modules_traits.R +0 -0
  103. /package/data/{workflows → skills}/coexpression-network/scripts/export_wgcna_results.R +0 -0
  104. /package/data/{workflows → skills}/coexpression-network/scripts/identify_hub_genes.R +0 -0
  105. /package/data/{workflows → skills}/coexpression-network/scripts/load_example_data.R +0 -0
  106. /package/data/{workflows → skills}/coexpression-network/scripts/module_enrichment.R +0 -0
  107. /package/data/{workflows → skills}/coexpression-network/scripts/pick_soft_power.R +0 -0
  108. /package/data/{workflows → skills}/coexpression-network/scripts/plot_all_wgcna.R +0 -0
  109. /package/data/{workflows → skills}/coexpression-network/scripts/plot_eigengene_heatmap.R +0 -0
  110. /package/data/{workflows → skills}/coexpression-network/scripts/plot_hub_genes.R +0 -0
  111. /package/data/{workflows → skills}/coexpression-network/scripts/plot_module_dendrogram.R +0 -0
  112. /package/data/{workflows → skills}/coexpression-network/scripts/plotting_helpers.R +0 -0
  113. /package/data/{workflows → skills}/coexpression-network/scripts/prepare_wgcna_data.R +0 -0
  114. /package/data/{workflows → skills}/coexpression-network/scripts/wgcna_workflow.R +0 -0
  115. /package/data/{workflows → skills}/experimental-design-statistics/SKILL.md +0 -0
  116. /package/data/{workflows → skills}/experimental-design-statistics/references/batch_effect_mitigation.md +0 -0
  117. /package/data/{workflows → skills}/experimental-design-statistics/references/cv_tissue_database.csv +0 -0
  118. /package/data/{workflows → skills}/experimental-design-statistics/references/experimental_design_best_practices.md +0 -0
  119. /package/data/{workflows → skills}/experimental-design-statistics/references/multiple_testing_guide.md +0 -0
  120. /package/data/{workflows → skills}/experimental-design-statistics/references/power_analysis_guidelines.md +0 -0
  121. /package/data/{workflows → skills}/experimental-design-statistics/references/qc_guidelines.md +0 -0
  122. /package/data/{workflows → skills}/experimental-design-statistics/references/software_requirements.md +0 -0
  123. /package/data/{workflows → skills}/experimental-design-statistics/references/troubleshooting_guide.md +0 -0
  124. /package/data/{workflows → skills}/experimental-design-statistics/scripts/batch_assignment.R +0 -0
  125. /package/data/{workflows → skills}/experimental-design-statistics/scripts/batch_validation.R +0 -0
  126. /package/data/{workflows → skills}/experimental-design-statistics/scripts/export_design.R +0 -0
  127. /package/data/{workflows → skills}/experimental-design-statistics/scripts/load_example_data.R +0 -0
  128. /package/data/{workflows → skills}/experimental-design-statistics/scripts/multiple_testing.R +0 -0
  129. /package/data/{workflows → skills}/experimental-design-statistics/scripts/plot_power_curves.R +0 -0
  130. /package/data/{workflows → skills}/experimental-design-statistics/scripts/power_atacseq.R +0 -0
  131. /package/data/{workflows → skills}/experimental-design-statistics/scripts/power_pilot_based.R +0 -0
  132. /package/data/{workflows → skills}/experimental-design-statistics/scripts/power_rnaseq.R +0 -0
  133. /package/data/{workflows → skills}/experimental-design-statistics/scripts/sample_size_de.R +0 -0
  134. /package/data/{workflows → skills}/experimental-design-statistics/scripts/sample_size_scrna.R +0 -0
  135. /package/data/{workflows → skills}/functional-enrichment-from-degs/SKILL.md +0 -0
  136. /package/data/{workflows → skills}/functional-enrichment-from-degs/references/database_guide.md +0 -0
  137. /package/data/{workflows → skills}/functional-enrichment-from-degs/references/decision-guide.md +0 -0
  138. /package/data/{workflows → skills}/functional-enrichment-from-degs/references/gsea_ora_comparison.md +0 -0
  139. /package/data/{workflows → skills}/functional-enrichment-from-degs/references/gsea_ora_validation_framework.md +0 -0
  140. /package/data/{workflows → skills}/functional-enrichment-from-degs/references/interpretation_guidelines.md +0 -0
  141. /package/data/{workflows → skills}/functional-enrichment-from-degs/references/method-reference.md +0 -0
  142. /package/data/{workflows → skills}/functional-enrichment-from-degs/scripts/export_results.R +0 -0
  143. /package/data/{workflows → skills}/functional-enrichment-from-degs/scripts/generate_plots.R +0 -0
  144. /package/data/{workflows → skills}/functional-enrichment-from-degs/scripts/get_msigdb_genesets.R +0 -0
  145. /package/data/{workflows → skills}/functional-enrichment-from-degs/scripts/load_de_results.R +0 -0
  146. /package/data/{workflows → skills}/functional-enrichment-from-degs/scripts/load_example_data.R +0 -0
  147. /package/data/{workflows → skills}/functional-enrichment-from-degs/scripts/prepare_gene_lists.R +0 -0
  148. /package/data/{workflows → skills}/functional-enrichment-from-degs/scripts/run_gsea.R +0 -0
  149. /package/data/{workflows → skills}/functional-enrichment-from-degs/scripts/run_ora.R +0 -0
  150. /package/data/{workflows → skills}/genetic-variant-annotation/SKILL.md +0 -0
  151. /package/data/{workflows → skills}/genetic-variant-annotation/references/auto_installation_implementation.md +0 -0
  152. /package/data/{workflows → skills}/genetic-variant-annotation/references/consequence_terms.md +0 -0
  153. /package/data/{workflows → skills}/genetic-variant-annotation/references/filtering_strategies.md +0 -0
  154. /package/data/{workflows → skills}/genetic-variant-annotation/references/installation_guide.md +0 -0
  155. /package/data/{workflows → skills}/genetic-variant-annotation/references/pathogenicity_interpretation.md +0 -0
  156. /package/data/{workflows → skills}/genetic-variant-annotation/references/qc_guidelines.md +0 -0
  157. /package/data/{workflows → skills}/genetic-variant-annotation/references/snpeff_best_practices.md +0 -0
  158. /package/data/{workflows → skills}/genetic-variant-annotation/references/tool_selection_guide.md +0 -0
  159. /package/data/{workflows → skills}/genetic-variant-annotation/references/troubleshooting_guide.md +0 -0
  160. /package/data/{workflows → skills}/genetic-variant-annotation/references/vep_best_practices.md +0 -0
  161. /package/data/{workflows → skills}/genetic-variant-annotation/scripts/annotate_genes.py +0 -0
  162. /package/data/{workflows → skills}/genetic-variant-annotation/scripts/export_results.py +0 -0
  163. /package/data/{workflows → skills}/genetic-variant-annotation/scripts/filter_variants.py +0 -0
  164. /package/data/{workflows → skills}/genetic-variant-annotation/scripts/install_tools.py +0 -0
  165. /package/data/{workflows → skills}/genetic-variant-annotation/scripts/load_example_data.py +0 -0
  166. /package/data/{workflows → skills}/genetic-variant-annotation/scripts/parse_snpeff_output.py +0 -0
  167. /package/data/{workflows → skills}/genetic-variant-annotation/scripts/parse_vep_output.py +0 -0
  168. /package/data/{workflows → skills}/genetic-variant-annotation/scripts/plot_variant_distribution.py +0 -0
  169. /package/data/{workflows → skills}/genetic-variant-annotation/scripts/prioritize_variants.py +0 -0
  170. /package/data/{workflows → skills}/genetic-variant-annotation/scripts/run_snpeff.py +0 -0
  171. /package/data/{workflows → skills}/genetic-variant-annotation/scripts/run_vep.py +0 -0
  172. /package/data/{workflows → skills}/genetic-variant-annotation/scripts/select_tool.py +0 -0
  173. /package/data/{workflows → skills}/genetic-variant-annotation/scripts/test_complete_workflow.py +0 -0
  174. /package/data/{workflows → skills}/genetic-variant-annotation/scripts/test_pickle_load.py +0 -0
  175. /package/data/{workflows → skills}/genetic-variant-annotation/scripts/validate_vcf.py +0 -0
  176. /package/data/{workflows → skills}/genetic-variant-annotation/scripts/verify_changes.py +0 -0
  177. /package/data/{workflows → skills}/grn-pyscenic/SKILL.md +0 -0
  178. /package/data/{workflows → skills}/grn-pyscenic/references/cli_interface.md +0 -0
  179. /package/data/{workflows → skills}/grn-pyscenic/references/database_downloads.md +0 -0
  180. /package/data/{workflows → skills}/grn-pyscenic/scripts/export_all.py +0 -0
  181. /package/data/{workflows → skills}/grn-pyscenic/scripts/generate_report.py +0 -0
  182. /package/data/{workflows → skills}/grn-pyscenic/scripts/integrate_with_adata.py +0 -0
  183. /package/data/{workflows → skills}/grn-pyscenic/scripts/load_example_data.py +0 -0
  184. /package/data/{workflows → skills}/grn-pyscenic/scripts/load_expression_data.py +0 -0
  185. /package/data/{workflows → skills}/grn-pyscenic/scripts/plot_regulon_visualizations.py +0 -0
  186. /package/data/{workflows → skills}/grn-pyscenic/scripts/run_grn_workflow.py +0 -0
  187. /package/data/{workflows → skills}/gwas-to-function-twas/SKILL.md +0 -0
  188. /package/data/{workflows → skills}/gwas-to-function-twas/references/fusion_best_practices.md +0 -0
  189. /package/data/{workflows → skills}/gwas-to-function-twas/references/installation-guide.md +0 -0
  190. /package/data/{workflows → skills}/gwas-to-function-twas/references/ldsc_qc_guidelines.md +0 -0
  191. /package/data/{workflows → skills}/gwas-to-function-twas/references/spredixxcan_best_practices.md +0 -0
  192. /package/data/{workflows → skills}/gwas-to-function-twas/references/therapeutic_interpretation_guide.md +0 -0
  193. /package/data/{workflows → skills}/gwas-to-function-twas/references/tissue_reference_guide.md +0 -0
  194. /package/data/{workflows → skills}/gwas-to-function-twas/references/troubleshooting_guide.md +0 -0
  195. /package/data/{workflows → skills}/gwas-to-function-twas/references/twas_hub_validation_guide.md +0 -0
  196. /package/data/{workflows → skills}/gwas-to-function-twas/scripts/colocalization_analysis.py +0 -0
  197. /package/data/{workflows → skills}/gwas-to-function-twas/scripts/druggability_scoring.py +0 -0
  198. /package/data/{workflows → skills}/gwas-to-function-twas/scripts/export_results.py +0 -0
  199. /package/data/{workflows → skills}/gwas-to-function-twas/scripts/integrate_variant_annotation.py +0 -0
  200. /package/data/{workflows → skills}/gwas-to-function-twas/scripts/interpret_therapeutic_direction.py +0 -0
  201. /package/data/{workflows → skills}/gwas-to-function-twas/scripts/mendelian_randomization.py +0 -0
  202. /package/data/{workflows → skills}/gwas-to-function-twas/scripts/multilayer_direction_analysis.py +0 -0
  203. /package/data/{workflows → skills}/gwas-to-function-twas/scripts/plot_twas_results.py +0 -0
  204. /package/data/{workflows → skills}/gwas-to-function-twas/scripts/run_fusion.py +0 -0
  205. /package/data/{workflows → skills}/gwas-to-function-twas/scripts/run_smultixcan.py +0 -0
  206. /package/data/{workflows → skills}/gwas-to-function-twas/scripts/run_spredixxcan.py +0 -0
  207. /package/data/{workflows → skills}/gwas-to-function-twas/scripts/select_reference_panel.py +0 -0
  208. /package/data/{workflows → skills}/gwas-to-function-twas/scripts/validate_gwas_sumstats.py +0 -0
  209. /package/data/{workflows → skills}/gwas-to-function-twas/scripts/validate_with_twas_hub.py +0 -0
  210. /package/data/{workflows → skills}/lasso-biomarker-panel/SKILL.md +0 -0
  211. /package/data/{workflows → skills}/lasso-biomarker-panel/references/decision-guide.md +0 -0
  212. /package/data/{workflows → skills}/lasso-biomarker-panel/references/lasso-reference.md +0 -0
  213. /package/data/{workflows → skills}/lasso-biomarker-panel/references/validation-guide.md +0 -0
  214. /package/data/{workflows → skills}/lasso-biomarker-panel/scripts/biological_interpretation.R +0 -0
  215. /package/data/{workflows → skills}/lasso-biomarker-panel/scripts/biomarker_plots.R +0 -0
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