ucscXena/xena-analysis-grails

Issues

• create server docker file

  #49 opened 4 years ago by nathandunn
  0

• add admin screen (in web) to change names and make public for admin (can use HS256)

  #48 opened 4 years ago by nathandunn
  0

• verify signed RS256

  #47 opened 4 years ago by nathandunn
  0

• authenticate grails server with GitHub - so users only see what they are doing and only allow some to do upload

  #39 opened 4 years ago by nathandunn
  18

• speed up results for large pathways (cache, filter)?

  #22 opened 4 years ago by nathandunn
  2

• upload TCGA geneset again

  #44 opened 4 years ago by nathandunn
  0

• pull down more proper go slims and analyze

  #16 opened 4 years ago by nathandunn
  5

• fork processes based on # of processors / 2 with a minimum of 1

  #41 opened 4 years ago by nathandunn
  0

• find global mean and stdev for activity z-scores

  #42 opened 4 years ago by nathandunn
  0

• add delete gmt

  #38 opened 4 years ago by nathandunn
  0

• build out analysis server in EC2

  #40 opened 4 years ago by nathandunn
  0

• convert default BPA Geneset to GMT

  #37 opened 4 years ago by nathandunn
  3

• fix key not found for the largest genesets

  #36 opened 4 years ago by nathandunn
  0

• fix sample order for ALL pathways

  #34 opened 4 years ago by nathandunn
  0

• ignores first line of the uploaded GMT

  #33 opened 4 years ago by nathandunn
  0

• when processing the "names" field seems to disappear for a moment

  #32 opened 4 years ago by nathandunn
  0

• optimize batch upload speed

  #21 opened 4 years ago by nathandunn
  0

• need to add local raw gene expression back (tabs) for BPA analysis

  #30 opened 4 years ago by nathandunn
  0

• speed up "names" method

  #29 opened 4 years ago by nathandunn
  0

• handle SAMPLE lists for calculation of pathway and gene expression (probably done) scores

  #28 opened 4 years ago by nathandunn
  0

• calculate per-gene pathway activity per GMT

  #23 opened 4 years ago by nathandunn
  0

• create tpm z-normalized tpm files

  #25 opened 4 years ago by nathandunn
  0

• allow processing of ALL Cohorts for a GMT

  #19 opened 4 years ago by nathandunn
  0

• store geneset count

  #17 opened 4 years ago by nathandunn
  0

• server-side github actions

  #12 opened 4 years ago by nathandunn
  0

• verify changing GMT with partial sub cohorts (detect difference)

  #9 opened 4 years ago by nathandunn
  0

• allow change of sub cohorts for custom gene sets for upload and server-side analysis

  #6 opened 4 years ago by nathandunn
  0

• generate tpm download should use post

  #13 opened 4 years ago by nathandunn
  0

• fix validation error - upload client-analysis versus server analysis

  #10 opened 4 years ago by nathandunn
  8

• changing GMT and cohort should and changing back should evaluate properly

  #8 opened 4 years ago by nathandunn
  1

• changing GMT should not re-evaluate

  #7 opened 4 years ago by nathandunn
  0

• do output analysis on the server

  #3 opened 4 years ago by nathandunn
  0

• support larger files: move to postgresql to support inserting more data or give H2 more memory or use File-system

  #2 opened 4 years ago by nathandunn
  0