@datagrok/proteomics 1.0.1 → 1.2.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (116) hide show
  1. package/CHANGELOG.md +52 -3
  2. package/CLAUDE.md +178 -0
  3. package/README.md +195 -3
  4. package/detectors.js +152 -9
  5. package/dist/package-test.js +1 -1744
  6. package/dist/package-test.js.map +1 -1
  7. package/dist/package.js +1 -146
  8. package/dist/package.js.map +1 -1
  9. package/docs/personas-and-capabilities.md +165 -0
  10. package/files/demo/README.md +264 -0
  11. package/files/demo/cptac-spike-in.txt +1571 -0
  12. package/files/demo/enrichment-demo.csv +120 -0
  13. package/files/demo/fragpipe-smoke-test.tsv +11 -0
  14. package/files/demo/proteinGroups.txt +28 -0
  15. package/files/demo/spectronaut-hye-candidates.tsv +94 -0
  16. package/files/demo/spectronaut-hye-demo.tsv +8761 -0
  17. package/files/demo/spectronaut-hye-mix.tsv +8761 -0
  18. package/files/demo/spectronaut-hye-precursor-golden.json +938 -0
  19. package/files/demo/spectronaut-hye-precursor-golden.tsv +235 -0
  20. package/files/demo/spectronaut-hye-precursor.tsv +493 -0
  21. package/images/enrichment-crosslink.png +0 -0
  22. package/images/enrichment-term-selected.png +0 -0
  23. package/images/hero.png +0 -0
  24. package/images/pipeline.svg +80 -0
  25. package/package.json +87 -63
  26. package/scripts/deqms_de.R +60 -0
  27. package/scripts/limma_de.R +42 -0
  28. package/scripts/vsn_normalize.R +19 -0
  29. package/src/analysis/differential-expression.ts +450 -0
  30. package/src/analysis/enrichment-export.ts +101 -0
  31. package/src/analysis/enrichment.ts +602 -0
  32. package/src/analysis/experiment-setup.ts +199 -0
  33. package/src/analysis/imputation.ts +407 -0
  34. package/src/analysis/log2-scale.ts +139 -0
  35. package/src/analysis/normalization.ts +255 -0
  36. package/src/analysis/pca.ts +254 -0
  37. package/src/analysis/spc-storage.ts +515 -0
  38. package/src/analysis/spc.ts +544 -0
  39. package/src/analysis/subcellular-location.ts +431 -0
  40. package/src/demo/enrichment-demo.ts +94 -0
  41. package/src/demo/proteomics-demo.ts +123 -0
  42. package/src/global.d.ts +15 -0
  43. package/src/menu.ts +133 -0
  44. package/src/package-api.ts +136 -14
  45. package/src/package-test.ts +45 -20
  46. package/src/package.g.ts +161 -0
  47. package/src/package.ts +1029 -17
  48. package/src/panels/protein-focus.ts +63 -0
  49. package/src/panels/published-analysis-panel.ts +151 -0
  50. package/src/panels/uniprot-panel.ts +349 -0
  51. package/src/parsers/fragpipe-parser.ts +200 -0
  52. package/src/parsers/generic-parser.ts +197 -0
  53. package/src/parsers/maxquant-parser.ts +162 -0
  54. package/src/parsers/shared-utils.ts +163 -0
  55. package/src/parsers/spectronaut-candidates-parser.ts +307 -0
  56. package/src/parsers/spectronaut-parser.ts +604 -0
  57. package/src/publishing/assert-published-shape.ts +260 -0
  58. package/src/publishing/post-open-recovery.ts +104 -0
  59. package/src/publishing/publish-project.ts +515 -0
  60. package/src/publishing/publish-settings.ts +59 -0
  61. package/src/publishing/publish-state.ts +316 -0
  62. package/src/publishing/share-dialog.ts +171 -0
  63. package/src/publishing/trim-dataframe.ts +247 -0
  64. package/src/tests/analysis.ts +658 -0
  65. package/src/tests/enrichment-export.ts +61 -0
  66. package/src/tests/enrichment-visualization.ts +340 -0
  67. package/src/tests/enrichment.ts +224 -0
  68. package/src/tests/fragpipe-e2e.ts +74 -0
  69. package/src/tests/fragpipe-parser.ts +147 -0
  70. package/src/tests/gene-label-resolver.ts +387 -0
  71. package/src/tests/generic-parser.ts +152 -0
  72. package/src/tests/group-mean-correlation.ts +139 -0
  73. package/src/tests/log2-scale.ts +93 -0
  74. package/src/tests/organisms.ts +56 -0
  75. package/src/tests/parsers.ts +182 -0
  76. package/src/tests/publish-roundtrip.ts +584 -0
  77. package/src/tests/publish-spike.ts +377 -0
  78. package/src/tests/qc-dashboard.ts +210 -0
  79. package/src/tests/smart-pathway-filter.ts +193 -0
  80. package/src/tests/spc-formula-lines-spike.ts +129 -0
  81. package/src/tests/spc.ts +640 -0
  82. package/src/tests/spectronaut-candidates-e2e.ts +140 -0
  83. package/src/tests/spectronaut-candidates-parser.ts +398 -0
  84. package/src/tests/spectronaut-parser.ts +668 -0
  85. package/src/tests/subcellular-location.ts +361 -0
  86. package/src/tests/uniprot-panel.ts +202 -0
  87. package/src/tests/volcano.ts +603 -0
  88. package/src/utils/column-detection.ts +28 -0
  89. package/src/utils/gene-label-resolver.ts +443 -0
  90. package/src/utils/organisms.ts +82 -0
  91. package/src/utils/proteomics-types.ts +30 -0
  92. package/src/viewers/enrichment-viewers.ts +274 -0
  93. package/src/viewers/group-mean-correlation.ts +218 -0
  94. package/src/viewers/heatmap.ts +168 -0
  95. package/src/viewers/pca-plot.ts +169 -0
  96. package/src/viewers/qc-computations.ts +266 -0
  97. package/src/viewers/qc-dashboard.ts +176 -0
  98. package/src/viewers/spc-dashboard.ts +755 -0
  99. package/src/viewers/volcano.ts +690 -0
  100. package/test-console-output-1.log +2055 -0
  101. package/test-record-1.mp4 +0 -0
  102. package/tools/derive-precursor-golden-sidecar.mjs +81 -0
  103. package/tools/generate-enrichment-fixture.sh +160 -0
  104. package/tools/generate-spectronaut-candidates-fixture.mjs +212 -0
  105. package/tools/generate-spectronaut-precursor-fixture.mjs +128 -0
  106. package/tools/spectronaut-aggregate.sh +46 -0
  107. package/tools/spectronaut-aggregate.sql +80 -0
  108. package/tsconfig.json +18 -71
  109. package/webpack.config.js +86 -45
  110. package/.eslintignore +0 -1
  111. package/.eslintrc.json +0 -56
  112. package/LICENSE +0 -674
  113. package/package.png +0 -0
  114. package/scripts/number_antibody.py +0 -190
  115. package/scripts/number_antibody_abnumber.py +0 -177
  116. package/scripts/number_antibody_anarci.py +0 -200
package/files/demo/spectronaut-hye-precursor-golden.tsv ADDED
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228
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229
+ P00028 CondB 3 run_CondB_3 1028.0 0.001
230
+ P00030 CondB 1 run_CondB_1 1030.0 0.001
231
+ P00031 CondA 1 run_CondA_1 1031.0 0.001
232
+ P00032 CondB 3 run_CondB_3 1032.0 0.001
233
+ P00034 CondA 3 run_CondA_3 1034.0 0.001
234
+ P00035 CondB 3 run_CondB_3 1035.0 0.001
235
+ P70003 CondB 3 run_CondB_3 6600.0