ucscXena/XenaGoWidget

Issues

• add GMT limit to 100 pathways for upload

  #702 opened 4 years ago by nathandunn
  0

• CVN and mutation should use a transparent background or draw white on their background?

  #740 opened 4 years ago by nathandunn
  1

• add PANCAN to default CNV / Mutation pathways

  #741 opened 4 years ago by nathandunn
  0

• buttons do not work with Xena in hover area

  #737 opened 4 years ago by nathandunn
  0

• remove console logging and linting

  #735 opened 4 years ago by nathandunn
  0

• show list of pathways available when going from dev xena to geneset widget in wizard screen

  #677 opened 4 years ago by nathandunn
  1

• fix nav bar with consistent layout, color and, theme

  #731 opened 4 years ago by nathandunn
  0

• surround each section in gray (no arrows down)

  #730 opened 4 years ago by nathandunn
  0

• make analysis part of fetch results

  #729 opened 4 years ago by nathandunn
  0

• put method in URL / expression

  #727 opened 4 years ago by nathandunn
  0

• remove server records if using Paradign IPL / Regulon and reset to `Default`

  #726 opened 4 years ago by nathandunn
  0

• disable instead of remove "upload"

  #723 opened 4 years ago by nathandunn
  0

• call default "public"

  #724 opened 4 years ago by nathandunn
  0

• a little bit of yellow bar is still at the top on safari

  #725 opened 4 years ago by nathandunn
  0

• remove "-" for non-admin users not looking at their own stuff and logged out users

  #722 opened 4 years ago by nathandunn
  0

• update app for multiple productions

  #719 opened 4 years ago by nathandunn
  1

• configure nwb for multiple build types

  #718 opened 4 years ago by nathandunn
  0

• rename gensets with proper labels on production and/or allow editing the names

  #710 opened 4 years ago by nathandunn
  0

• add geneset edit back for local gensets to allow downloads, etc.

  #709 opened 4 years ago by nathandunn
  0

• remove option to upload from paradigm IPL and regulon

  #712 opened 4 years ago by nathandunn
  0

• put question mark / info within one of the yellow boxes

  #711 opened 4 years ago by nathandunn
  0

• if "<0" then hide in assigned . . . and in hover box

  #708 opened 4 years ago by nathandunn
  2

• remove "View in Xena" if a server component . . not sure about open genes, though

  #713 opened 4 years ago by nathandunn
  0

• add a copy link URL button on the far left

  #714 opened 4 years ago by nathandunn
  0

• move +/-/up buttons to LHS

  #715 opened 4 years ago by nathandunn
  0

• link into Xena seems to be broken or remove

  #701 opened 4 years ago by nathandunn
  1

• error on reload, needs to fetch results

  #706 opened 4 years ago by nathandunn
  1

• make a very big FIND button off to the right

  #703 opened 4 years ago by nathandunn
  0

• replace Suzi's tcga with LP's GMT

  #704 opened 4 years ago by nathandunn
  0

• use global Pathway Z-Score fixed across any analysis use global mean (0) and 1 or 2 stdev on either side across z-scores

  #700 opened 4 years ago by nathandunn
  2

• can we remove a custom gene set?

  #694 opened 4 years ago by nathandunn
  1

• add gene set by gene? (broken)

  #693 opened 4 years ago by nathandunn
  0

• disallow edit on "custom" gene sets

  #698 opened 4 years ago by nathandunn
  0

• allow configurable env for server connection from client

  #696 opened 4 years ago by nathandunn
  0

• move genesets out of src/data . . into server-side data

  #692 opened 4 years ago by nathandunn
  0

• fix gene sample order, fix pathway and gene sample color - validate a custom GMT using Default to make sure it is the same

  #684 opened 4 years ago by nathandunn
  12

• fix testing so doesn't arbitrarily fail

  #689 opened 4 years ago by nathandunn
  0

• re-validate z-scores after change

  #687 opened 4 years ago by nathandunn
  0

• fix gene set and gene hover label

  #685 opened 4 years ago by nathandunn
  0

• add local raw "gene expression raw" scores for doing BPA analysis

  #683 opened 4 years ago by nathandunn
  0

• if pathway dropdown description is long, it extends stuff too far

  #682 opened 4 years ago by nathandunn
  0

• integrate new gene expression cohort Z-values with in cohort server

  #681 opened 4 years ago by nathandunn
  0

• export gene TPM files to export to Jing

  #679 opened 4 years ago by nathandunn
  1

• redo calculations to generate Z-Score over all sample values (TPMs) and store Z-scores

  #670 opened 4 years ago by nathandunn
  0

• default genesets should ALSO have the GO terms

  #674 opened 4 years ago by nathandunn
  2

• update pathways to use "official" GOlabel terms

  #675 opened 4 years ago by nathandunn
  1

• hover geneset labels should have goid for default and custom gene sets when available

  #676 opened 4 years ago by nathandunn
  0

• add number of pathways to geneset drop-down

  #668 opened 4 years ago by nathandunn
  0

• Improve UI

  #671 opened 4 years ago by 2580ayush2580
  4

• recover GO Ids for custom gene sets

  #669 opened 4 years ago by nathandunn
  0