@sjcrh/proteinpaint-server 2.30.4 → 2.30.5

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 (51) hide show
  1. package/genome/hg19.js +3 -3
  2. package/genome/hg38.js +3 -3
  3. package/genome/hg38.test.js +3 -3
  4. package/package.json +1 -1
  5. package/routes/burden.ts +5 -2
  6. package/routes/gdc.maf.ts +39 -26
  7. package/routes/gdc.mafBuild.ts +5 -5
  8. package/routes/hicdata.ts +113 -0
  9. package/routes/hicstat.ts +55 -0
  10. package/routes/termdb.categories.ts +30 -6
  11. package/routes/termdb.getpercentile.ts +117 -0
  12. package/routes/termdb.termbyid.ts +5 -1
  13. package/server.js +1 -1
  14. package/src/serverconfig.js +0 -19
  15. package/cards/2dmaf.json +0 -37
  16. package/cards/README.md +0 -15
  17. package/cards/ai.json +0 -37
  18. package/cards/arc.json +0 -34
  19. package/cards/ase.json +0 -99
  20. package/cards/bam.json +0 -264
  21. package/cards/bampile.json +0 -22
  22. package/cards/bedj.json +0 -304
  23. package/cards/bigwig.json +0 -70
  24. package/cards/citations.json +0 -39
  25. package/cards/civicBtn.json +0 -15
  26. package/cards/databrowser.json +0 -276
  27. package/cards/disco.json +0 -69
  28. package/cards/dnanexusTips.txt +0 -221
  29. package/cards/exprank.json +0 -64
  30. package/cards/featuredDatasets.json +0 -84
  31. package/cards/fusioneditor.json +0 -34
  32. package/cards/gdcbam.json +0 -23
  33. package/cards/genefusion.json +0 -57
  34. package/cards/genomepaint.json +0 -122
  35. package/cards/hic.json +0 -79
  36. package/cards/index.json +0 -327
  37. package/cards/junction.json +0 -98
  38. package/cards/lollipop.json +0 -327
  39. package/cards/maf.timeline.json +0 -19
  40. package/cards/mavb.json +0 -47
  41. package/cards/nciGdcBtn.json +0 -21
  42. package/cards/pcmBtn.json +0 -16
  43. package/cards/ped2Btn.json +0 -16
  44. package/cards/pgv.json +0 -59
  45. package/cards/scatterplot.json +0 -31
  46. package/cards/singlecell.json +0 -25
  47. package/cards/study.json +0 -34
  48. package/cards/survivorBtn.json +0 -18
  49. package/cards/svview.txt +0 -101
  50. package/cards/tkFeatures.json +0 -92
  51. package/cards/tklist.json +0 -27
package/cards/databrowser.json DELETED
@@ -1,276 +0,0 @@
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- {
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- "intro": "By uploading a dictionary in the Data Browser, one can explore the structure of their custom data. <br><br>Options to upload sample annotation and other data types are in development.",
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- "ppcalls":[
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- {
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- "isUi": true,
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- "runargs": {
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- "noheader": true,
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- "nobox": 1,
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- "parseurl": false,
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- "tkui": "databrowser"
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- }
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- },
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- {
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- "label": "Custom Data",
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- "download":"https://proteinpaint.stjude.org/ppdemo/databrowser/dictionaryDemoData.tar.gz",
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- "runargs": {
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- "noheader": true,
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- "nobox":true,
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- "mass":{
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- "state": {
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- "vocab": {
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- "terms": [
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- {
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- "id": "Demographic",
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- "isleaf": false,
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- "name": "Demographic",
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- "parent_id": null
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- },
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- {
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- "id": "Prognosis",
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- "isleaf": false,
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- "name": "Prognosis",
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- "parent_id": null
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- },
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- {
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- "groupsetting": {
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- "disabled": true
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- },
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- "id": "Gender",
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- "isleaf": true,
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- "name": "Gender",
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- "parent_id": "Demographic",
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- "type": "categorical",
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- "values": {
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- "Female": {
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- "color": "pink",
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- "key": "Female",
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- "label": "Female"
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- },
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- "Male": {
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- "color": "lightblue",
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- "key": "Male",
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- "label": "Male"
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- }
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- }
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- },
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- {
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- "bins": {
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- "default": {
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- "bin_size": 0.5,
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- "first_bin": {
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- "stop": 0.5
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- },
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- "rounding": ".1f",
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- "startinclusive": true,
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- "type": "regular-bin"
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- }
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- },
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- "id": "Age",
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- "isleaf": true,
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- "parent_id": "Demographic",
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- "name": "Age at Diagnosis",
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- "type": "float",
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- "values": {}
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- },
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- {
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- "type": "categorical",
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- "values": {
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- "3-6 yrs": {
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- "key": "3-6 yrs",
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- "label": "3-6 yrs",
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- "color": "green"
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- },
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- "<3 yrs": {
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- "key": "<3 yrs",
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- "label": "<3 yrs",
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- "color": "orange"
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- }
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- },
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- "isleaf": true,
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- "id": "Age Group",
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- "name": "Age Group",
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- "parent_id": "Demographic",
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- "groupsetting": {
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- "disabled": true
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- }
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- },
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- {
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- "type": "categorical",
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- "values": {
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- "Dead ": {
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- "key": "Dead ",
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- "label": "Dead "
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- },
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- "Alive": {
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- "key": "Alive",
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- "label": "Alive"
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- }
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- },
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- "isleaf": true,
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- "id": "Alive/Dead",
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- "name": "Alive/Dead",
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- "parent_id": "Prognosis",
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- "groupsetting": {
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- "disabled": true
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- }
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- },
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- {
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- "groupsetting": {
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- "disabled": true
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- },
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- "id": "Progresssive Disease",
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- "isleaf": true,
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- "name": "Progresssive Disease",
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- "parent_id": "Prognosis",
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- "type": "categorical",
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- "values": {
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- "No": {
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- "color": "red",
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- "key": "No",
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- "label": "No"
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- },
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- "Yes": {
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- "color": "green",
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- "key": "Yes",
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- "label": "Yes"
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- }
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- }
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- }
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- ],
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- "sampleannotation": {
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- "0": {
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- "Age": 5,
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- "Gender": "Male",
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- "Alive/Dead": "Dead",
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- "Age Group": "3-6 yrs",
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- "Progresssive Disease": "No"
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- },
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- "1": {
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- "Age": 2,
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- "Gender": "Female",
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- "Alive/Dead": "Alive",
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- "Age Group": "<3 yrs",
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- "Progresssive Disease": "Yes"
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- },
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- "2": {
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- "Age": 4,
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- "Gender": "Male",
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- "Alive/Dead": "Alive",
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- "Age Group": "3-6 yrs",
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- "Progresssive Disease": "No"
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- },
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- "3": {
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- "Age": 6,
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- "Gender": "Male",
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- "Alive/Dead": "Alive",
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- "Age Group": "3-6 yrs",
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- "Progresssive Disease": "Yes"
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- },
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- "4": {
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- "Age": 5,
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- "Gender": "Male",
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- "Alive/Dead": "Alive",
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- "Age Group": "3-6 yrs",
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- "Progresssive Disease": "No"
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- },
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- "5": {
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- "Age": 4,
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- "Gender": "Male",
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- "Alive/Dead": "Alive",
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- "Age Group": "3-6 yrs",
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- "Progresssive Disease": "No"
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- },
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- "6": {
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- "Age": 2,
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- "Gender": "Male",
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- "Alive/Dead": "Alive",
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- "Age Group": "<3 yrs",
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- "Progresssive Disease": "No"
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- },
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- "7": {
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- "Age": 4,
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- "Gender": "Male",
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- "Alive/Dead": "Dead",
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- "Age Group": "3-6 yrs",
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- "Progresssive Disease": "Yes"
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- },
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- "8": {
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- "Age": 5,
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- "Gender": "Female",
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- "Alive/Dead": "Alive",
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- "Age Group": "3-6 yrs",
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- "Progresssive Disease": "Yes"
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- },
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- "9": {
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- "Age": 5,
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- "Gender": "Male",
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- "Alive/Dead": "Alive",
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- "Age Group": "3-6 yrs",
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- "Progresssive Disease": "No"
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- }
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- }
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- },
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- "plots": [{
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- "chartType": "dictionary"
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- }]
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- }
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- }
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- },
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- "testSpec": {
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- "timeout": 7000,
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- "expected": { "button": 1 }
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- }
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- },
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- {
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- "label": "Survivorship Study",
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- "runargs":{
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- "noheader": true,
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- "nobox":true,
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- "termdb":{
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- "state": {
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- "vocab": {
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- "dslabel": "SJLife",
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- "genome": "hg38"
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- }
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- }
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- }
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- },
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- "buttons": [
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- {
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- "name": "Survivorship Study Homepage",
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- "link": "https://survivorship.stjude.cloud/"
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- }
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- ],
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- "testSpec": {
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- "timeout": 7000,
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- "expected": { "input": 1, "button": 1 }
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- }
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- },
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- {
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- "label": "MSigDB",
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- "runargs":{
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- "noheader": true,
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- "nobox":true,
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- "termdb":{
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- "state": {
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- "vocab": {
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- "dslabel": "msigdb",
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- "genome": "hg38"
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- }
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- }
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- }
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- },
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- "buttons": [
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- {
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- "name": "MSigDB Homepage",
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- "link": "http://www.gsea-msigdb.org/gsea/msigdb/index.jsp"
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- }
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- ],
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- "testSpec": {
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- "timeout": 7000,
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- "expected": { "input": 1, "button": 1 }
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- }
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- }
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- ]
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- }
package/cards/disco.json DELETED
@@ -1,69 +0,0 @@
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- {
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- "ribbonMessage": "We're excited to announce our newest app, the <b>Disco Plot!</b>",
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- "ppcalls": [
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- {
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- "isUi": true,
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- "runargs": {
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- "noheader": true,
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- "nobox": 1,
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- "parseurl": false,
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- "tkui": "disco"
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- }
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- },
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- {
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- "message": "In this plot, all chromosomes of the genome are arranged in a circle. Multiple rings along the circle indicates example data points of mutation, copy number change, and structural variation/fusion events. Gene labels are based on mutation and sv/fusion events.",
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- "runargs": {
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- "noheader": true,
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- "nobox": true,
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- "genome": "hg38",
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- "disco": {
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- "mlst": [
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- {
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- "alt": "T",
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- "chr": "chr1",
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- "class": "M",
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- "dt": 1,
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- "gene": "H3F3A",
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- "isoform": "NM_002107",
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- "mname": "K28M",
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- "position": 226252135,
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- "ref": "A"
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- },
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- {
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- "dt": 4,
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- "chr": "chr1",
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- "start": 1,
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- "stop": 100000000,
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- "value": 0.5
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- },
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- {
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- "dt": 4,
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- "chr": "chr1",
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- "start": 100000000,
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- "stop": 200000000,
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- "value": -0.5
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- },
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- {
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- "chrA": "chr6",
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- "posA": 3067605,
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- "geneA": "MDC1",
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- "chrB": "chr12",
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- "posB": 61521661,
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- "geneB": "KMT2D",
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- "dt": 2,
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- "strandA": "+",
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- "strandB": "-"
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- }
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- ]
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- }
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- },
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- "testSpec": {
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- "button": 1,
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- "expected": {
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- "svg": 1,
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- "g": 2
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- }
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- }
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- }
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- ]
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- }
package/cards/dnanexusTips.txt DELETED
@@ -1,221 +0,0 @@
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- <div style="line-height: 1.5em; padding: 2vw; font-family: 'Lucida Grande', sans-serif;">
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-
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- <h1 style="margin: 5% 0% 2% 2%;">Using DNAnexus and ProteinPaint</h1>
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- <br>
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- <p style="font-style:oblique; font-weight: 300; margin: 0vw 5vw; text-align:center; color: #403f3f;">
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- DNAnexus provides a secure way to view unpublished/sensitive files and create tracks within ProteinPaint. Use the tips in the guide below for how to store files and create tracks in ProteinPaint.
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- </p>
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- <nav style="margin: 5% 0% 2% 2%;">
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- <ul style="list-style-type: none;">
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- <li><a href="#start">Getting Started</a></li>
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- <li><a href="#upload">Upload Files</a></li>
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- <li><a href="#link">Creating URLs</a></li>
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- <li><a href="#track">Create a Track</a></li>
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- <li><a href="#fileviewer">ProteinPaint Fileviewer</a></li>
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- </ul>
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- </nav>
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- <div style="margin: 3vw;">
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- <p style="margin-left: 2vw;">
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- This tutorial is specific to ProteinPaint. For more detailed information about DNAnexus, please see the <a href="https://documentation.dnanexus.com/" target="_blank"> documentation</a>.
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- </p>
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- <br>
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-
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-
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- <h2 id="start">Getting Started</h2>
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- <p style="margin-left: 2vw;">
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- <ul style="margin-left: 2vw;">
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- <li>
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- Create an account with DNAnexus. <a href="https://university.stjude.cloud/docs/genomics-platform/accounts-and-billing/" target="_blank">Follow the instructions from St. Jude Cloud</a>. Please direct questions regarding account set up to the St. Jude Cloud team (<a href="mailto:support@stjude.cloud?subject=Help Setting Up a DNAnexus Account">support@stjude.cloud</a>).
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- </li>
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- <li>
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- Create a token from the <a href="https://platform.dnanexus.com/" target="_self">DNAnexus platform</a>. See this link on how to generate an authentication <a href="https://documentation.dnanexus.com/user/login-and-logout#authentication-tokens" target="_blank">token</a>. Be sure to save the token!
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- </li>
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- <li>
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- Create a new project in DNAnexus with Azure (will not work with AWS funded projects). See the DNAnexus documentation <a href="https://documentation.dnanexus.com/getting-started/ui-quickstart#step-1-make-your-first-project" target="_blank">See the DNAnexus documentation</a> for instructions on how to set up a new project.
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- </li>
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- <li>
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- Install <span style="font-family:monospace; font-size:1.25em; opacity: 0.6;"> dx-toolkit</span> by following the <a href="https://documentation.dnanexus.com/downloads" target="_blank">DNAnexus documentation</a>.
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- </li>
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- </ul>
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- </p>
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- <p style="margin-left: 2vw;">
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- <strong>Tip</strong>: Uploading files from the command line is faster than from the web browser. Instructions for both methods are provided.
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- </p>
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- <br>
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- <br>
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-
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-
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- <h2 id="upload">Upload Files</h2>
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- <br>
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-
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- <h3>Command Line</h3>
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- <p style="margin-left: 2vw;">
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- All DNAnexus <span style="font-family:monospace; font-size:1.25em; opacity: 0.6;"> dx-toolkit</span> commands begin with <span style="font-family:monospace; font-size:1.25em; opacity: 0.6;"> dx</span>. A full list of commands to navigate through folders, copy files, etc. is available <a href="https://documentation.dnanexus.com/user/helpstrings-of-sdk-command-line-utilities" target="_blank">here</a>.
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- <br>
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- Login into DNAnexus with your authentication token:
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- <pre style="margin: 0vw 1vw; opacity: 0.6; white-space:pre-wrap;">
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- $ dx login --token MyAuthenicationToken
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- </pre>
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- </p>
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- <p style="margin-left: 2vw;">
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- A list of available projects will appear. Select the appropriate project from the number appearing in brackets:
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- <pre style="margin: 0vw 1vw; opacity: 0.6; white-space:pre-wrap;">
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- Available projects (CONTRIBUTE or higher):
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- [0]My_ProteinPaint_Project
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-
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- Pick a numbered choice: 0
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- </pre>
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- </p>
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- <p style="margin-left: 2vw;">
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- Upload all files to the project with the <a href="https://documentation.dnanexus.com/user/helpstrings-of-sdk-command-line-utilities#upload" target="_blank">dx upload</a> command.
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-
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- Unzip the FileViewer and upload it to the project with this command:
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- <pre style="margin: 0vw 1vw; opacity: 0.6; white-space:pre-wrap;">
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- $ dx upload --type FileViewer 'ProteinPaint (VCF, bigWig, BEDj, junction, BAM)'
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- </pre>
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- </p>
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- <br>
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-
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- <h3>DNAnexus Website</h3>
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- <p style="margin-left: 2vw;">
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- Uploading files through the DNAnexus website is easy but takes more time and processing power.
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- <ul style="margin-left: 2vw;">
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- <li>
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- Select the appropriate project
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- </li>
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- <li>
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- Click the Upload button. Upload all files and the FileViewer.
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- </li>
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- </ul>
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- </p>
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- <br>
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- <br>
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-
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-
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- <h2 id="link">Creating URLs</h2>
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- <br>
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-
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- <h3>Command line</h3>
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- <p style="margin-left: 2vw;">
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- While logged into DNAnexus on the command line, create a URL with the <span style="font-family:monospace; font-size:1.25em; opacity: 0.6;"> make_download_url</span> command. Specify the file and duration for the URL. The following is an example of a download URL command expiring in ten years. </p>
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- <pre style="margin: 0vw 1vw; opacity: 0.6; white-space:pre-wrap;">
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- dx make_download_url bigWigExample.bw -–duration 10y
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- </pre>
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- <p style="margin-left: 2vw;">
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- See the <a href='https://documentation.dnanexus.com/user/helpstrings-of-sdk-command-line-utilities#make_download_url' target='Extend URL'>DNAnexus documentation</a> for more information.
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- </p>
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- <br>
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-
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- <h3>DNAnexus Website</h3>
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- <p style="margin-left: 2vw;">
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- Creating the URL from the DNAnexus website is easy but the URL expires in 24 hours. Login to the DNAnexus website and navigate to the appropriate project.
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- <ul>
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- <li>
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- Find the file and hover the mouse on the far right of the screen until three dots appear.
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- <img style="width: 50vw; margin: 1vw 2vw;" src="https://proteinpaint.stjude.org/ppdemo/images/dnanexus_3dot_menu.png">
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- </li>
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- <li>
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- Select 'Download' from the menu
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- </li>
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- <li>
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- A popup 'Download Data' window will appear. Hover over the file to see the 'Get URL' icon (&#128279) on the right. Click on the (&#128279) icon.
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- </li>
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- <li>
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- The icon button will change to 'Copy URL'. Click to copy the link.
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- <img style="width: 50vw; margin: 1vw 2vw;" src="https://proteinpaint.stjude.org/ppdemo/images/dnanexus_copy_URL.png">
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- </li>
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- </ul>
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- Save the new URL. The next section describes how to create a ProteinPaint track using URL parameters.
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- </p>
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- <br>
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- <br>
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-
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-
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- <h2 id="track">Create a Track</h2>
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- <p style="margin-left: 2vw;">
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- Create a track from stringing together URL parameters described in this <a href='https://docs.google.com/document/d/1e0JVdcf1yQDZst3j77Xeoj_hDN72B6XZ1bo_cAd2rss/edit#heading=h.737pcqp1tlnt' target='URL param'>document</a>. <br><br>
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-
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- Start with "https://proteinpaint.stjude.org/?" and add the URL parameters separated by ampersands. In the example below, parameters for the genome, block, track name, and file URL to launch the genome browser. The final URL <a href="https://proteinpaint.stjude.org/?genome=hg19&block=1&bigwigurl=URL,https://proteinpaint.stjude.org/ppdemo/hg19/bigwig/file.bw">https://proteinpaint.stjude.org/?genome=hg19&block=1&bigwigurl=URL,https://proteinpaint.stjude.org/ppdemo/hg19/bigwig/file.bw</a>, launches this bigwig track.
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- <img style="width: 50vw; margin: 1vw 2vw;" src="https://proteinpaint.stjude.org/ppdemo/images/bigwig_url_ex.png">
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- </p>
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- <br>
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- <br>
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-
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-
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- <h2 id="fileviewer">ProteinPaint FileViewer</h2>
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- <p style="margin-left: 2vw;">The ProteinPaint FileViewer launches VCF, BigWig, JSON BED, Splice Junction, and BAM tracks from the DNAnexus website. Download the ProteinPaint FileViewer from the blue button below.</p>
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- <div style="margin:0vw 2vw; display: flex; justify-content: center; padding: 10px;">
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- <button type="button" onclick="window.open('https://proteinpaint.stjude.org/ppdemo/fileviewers/ProteinPaint%20(VCF,%20bigWig,%20BEDj,%20junction,%20BAM).gz','_self', 'download')" style="background-color: #d0e3ff; padding: 8px; border-radius: 3px; border: none; display: inline-block;margin: 0px 10px; font-size: 1.1em;">Download ProteinPaint FileViewer</button>
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- </div>
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- <br>
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-
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- <h3>Prepare Files</h3>
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- <p style="margin-left: 2vw;">
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- Ensure all files end with one of the following extensions:
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- <ul style="margin-left: 2vw;">
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- <li>
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- <span style="font-family:monospace; font-size:1.25em; opacity: 0.6;">.vcf.gz</span>
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- </li>
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- <li>
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- <span style="font-family:monospace; font-size:1.25em; opacity: 0.6;">.bw</span>
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- </li>
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- <li>
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- <span style="font-family:monospace; font-size:1.25em; opacity: 0.6;">.bedj.gz</span>
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- </li>
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- <li>
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- <span style="font-family:monospace; font-size:1.25em; opacity: 0.6;">.bam</span>
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- </li>
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- </ul>
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- </p>
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- <p style="margin-left: 2vw;">
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- Index files for VCF, bedj, and BAM are <strong>required</strong>.
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- <br><br>
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- Create the index file for the VCF, bedj and BAM files with the following commands. These commands require samtools, bcftools, and htslib packages. Download these packages <a href="http://www.htslib.org/download/" target="_blank">here</a>.
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- <br><br>
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- </p>
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- <div style="margin-left: 2vw;">
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- <p style="margin-left: 2vw;">
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- Index a VCF or bedj file with these commands:
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- <pre style="margin: 0vw 1vw; opacity: 0.6; white-space:pre-wrap;">
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- $ sort -k1,1 -k2,2n FILE > FILE.sorted
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- $ bgzip FILE.sorted
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- $ tabix -p bed FILE.sorted.gz
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- </pre>
184
- </p>
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- <p style="margin-left: 2vw;">
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- Index a BAM file with the following command:
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- <pre style="margin: 0vw 1vw; opacity: 0.6; white-space:pre-wrap;">
188
- $ samtools index bamFile.bam
189
- </pre>
190
- </div>
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- <br>
192
-
193
- <h3>Launch FileViewer</h3>
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- <p style="margin-left: 2vw;">
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- Open the DNAnexus website and navigate to the project.
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- <ul style="margin-left: 2vw;">
197
- <li>
198
- Click on the <span style="font-family:monospace; font-size:1.25em; opacity: 0.6;">ProteinPaint (VCF, bigWig, BEDj, junction, BAM)</span> FileViewer.
199
- </li>
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- <li>
201
- Select which files to visualize in ProteinPaint. Ensure to include index files.
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- <img style="width: 50vw; margin: 1vw 2vw;" src="https://proteinpaint.stjude.org/ppdemo/fileviewers/select_files.png">
203
- </li>
204
- <li>
205
- Click Launch Viewer in the bottom right of the window.
206
- </li>
207
- <li>
208
- The following interface will appear in the browser:
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-
210
- <img style="width: 20vw; margin: 1vw 4vw; display: block;" src="https://proteinpaint.stjude.org/ppdemo/fileviewers/interface.png">
211
-
212
- Select the reference genome. Then, enter a genomic position or search for a gene to launch the visualization. ProteinPaint will launch in a new tab, like the example below.<br>
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- <img style="width: 50vw; margin: 1vw 1vw;" src="https://proteinpaint.stjude.org/ppdemo/fileviewers/final.png">
214
- </li>
215
- </ul>
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- </p>
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- <p style="margin-left: 2vw;">
218
- <strong>Tip</strong>: The URL created from the FileViewer is only available while the tab is open. Once the tab is closed, repeat the steps in this section to launch the FileViewer again.
219
- </p>
220
- </div>
221
- </div>
package/cards/exprank.json DELETED
@@ -1,64 +0,0 @@
1
- {
2
- "ppcalls": [
3
- {
4
- "message": "<p style='line-height: 1.5em;'>In this example, <em>three</em> expression rank tracks are shown: rank, FPKM, and TPM. The first track displays the expression rank on a scale of 0 - 100%. The second FPKM track and third TPM track display values on a scale from zero to the highest rounded value, 0 - 9,775 and 0 - 3.9, respectively. Hover over the grey bars to see the annotation for each gene.<br><br>To change between expression rank and FPKM/TPM: <ul><li>Click on <span style='color:gray; text-decoration: none;'>CONFIG</span> on the right-hand side of the track</li><li>Change the radio button to either 'FPKM'/'TPM' or 'Rank of a group of samples.'</li></ul></p>",
5
- "datapreview": [
6
- {
7
- "file": "proteinpaint_demo/hg38/exprank/TCGA.fpkm.gz",
8
- "tabixQueryCoord": "chr8:127340055-128243343"
9
- }
10
- ],
11
- "runargs": {
12
- "parseurl": true,
13
- "block": true,
14
- "nobox": 1,
15
- "noheader": 1,
16
- "genome": "hg38",
17
- "position": "chr8:127340055-128243343",
18
- "nativetracks": "RefGene",
19
- "tracks": [
20
- {
21
- "type": "mdsexpressionrank",
22
- "file": "proteinpaint_demo/hg38/exprank/TCGA.fpkm.gz",
23
- "name": "TCGA-GS-A9TQ expression rank",
24
- "sample": "TCGA-GS-A9TQ",
25
- "barheight": 100
26
- },
27
- {
28
- "type": "mdsexpressionrank",
29
- "file": "proteinpaint_demo/hg38/exprank/TCGA.fpkm.gz",
30
- "name": "TCGA-GS-A9TQ gene FPKM",
31
- "sample": "TCGA-GS-A9TQ",
32
- "showrank": false,
33
- "gecfg": {"datatype":"FPKM"},
34
- "barheight": 100,
35
- "toppad": 20
36
- },
37
- {
38
- "type": "mdsexpressionrank",
39
- "file": "proteinpaint_demo/hg38/exprank/cardiomyocyte.fpkm.tpm.gz",
40
- "name": "Cardiomyocyte RNAseq TPM",
41
- "sample": "cardiomyocyte-avg",
42
- "showrank": false,
43
- "gecfg": {"datatype": "TPM"},
44
- "barheight": 100,
45
- "toppad": 20
46
- }
47
- ]
48
- },
49
- "testSpec": {
50
- "expected": {"rect": 5 }
51
- }
52
- }
53
- ],
54
- "buttons": [
55
- {
56
- "name": "Documentation",
57
- "link": "https://docs.google.com/document/d/1owXUQuqw5hBHFERm0Ria7anKtpyoPBaZY_MCiXXf5wE/edit#heading=h.q9ccqxkrh30s"
58
- },
59
- {
60
- "name": "Download Track File",
61
- "link": "https://proteinpaint.stjude.org/ppdemo/hg38/exprank/exprankDemoData.tar.gz"
62
- }
63
- ]
64
- }