GSEA-MSigDB/GSEA2.jl

Issues

• Match the 1 liners.

  #83 opened 5 months ago by KwatMDPhD
  1

• Rename to GSEA2.jl.

  #82 opened 5 months ago by KwatMDPhD
  3

• Enlarge axis titles

  #81 opened a year ago by KwatMDPhD
  0

• Write settings.

  #73 opened a year ago by KwatMDPhD
  0

• Remove 0.5 from `KLioM` and `KLioP`.

  #80 opened a year ago by KwatMDPhD
  0

• Highlight the peak(s) with `ks` and the area with the other algorithms.

  #77 opened a year ago by KwatMDPhD
  1

• Write instructions for `julia` interface.

  #76 opened a year ago by yang-dongxu
  2

• Make tutorials.

  #79 opened a year ago by KwatMDPhD
  0

• Build a graphic user interface.

  #78 opened a year ago by KwatMDPhD
  0

• Use `@warn` instead of `@error`.

  #75 opened a year ago by KwatMDPhD
  0

• Add normalization settings.

  #74 opened a year ago by KwatMDPhD
  0

• Make `gsea data-rank` plot.

  #72 opened a year ago by KwatMDPhD
  0

• Implement `gsea convert-gmt` and `gsea convert-gct-cls`.

  #71 opened a year ago by KwatMDPhD
  0

• Set individual exponent with `.json` or `.tsv`.

  #52 opened 3 years ago by ACastanza
  7

• Go with all JSON or all CLI interface.

  #70 opened a year ago by KwatMDPhD
  0

• Write out additional dict containing running enrichment score data for all sets

  #44 opened 2 years ago by ACastanza
  4

• Change Enrichment Plot Positive Color

  #53 opened 2 years ago by ACastanza
  8

• Make the new algorithm computation faster

  #67 opened 2 years ago by ACastanza
  2

• Fix feature y-axis

  #69 opened 2 years ago by KwatMDPhD
  0

• Debug `ks` and `cidac` plotting the same plots

  #68 opened 2 years ago by KwatMDPhD
  0

• Logic error in selecting which sets to plot

  #64 opened 2 years ago by ACastanza
  9

• Check the number of sets for plotting and more

  #65 opened 2 years ago by KwatMDPhD
  2

• Fix p-value adjustment

  #66 opened 2 years ago by KwatMDPhD
  2

• Plot a heat map or delete `plot/` for `data-ranks`

  #56 opened 2 years ago by KwatMDPhD
  0

• Use good .html format

  #63 opened 2 years ago by ACastanza
  13

• data-rank fails with error

  #62 opened 2 years ago by ACastanza
  5

• Remove temporary `PacakgeCompiler.jl`

  #60 opened 2 years ago by KwatMDPhD
  0

• 0.11.3 Fails to Build

  #61 opened 2 years ago by ACastanza
  3

• 0.11.2 extracted from tarball fails when running gsea -h

  #59 opened 2 years ago by ACastanza
  3

• 0.11.1 Build Tests Fail when building app tarball

  #58 opened 2 years ago by ACastanza
  3

• Error building docker container with 0.11.0

  #57 opened 2 years ago by ACastanza
  6

• For `data-ranks` output `set_x_sample_x_significance.tsv`

  #55 opened 3 years ago by KwatMDPhD
  1

• Consider flipping table, plot, and all

  #54 opened 3 years ago by KwatMDPhD
  0

• Make target_x_sample_x_number.tsv 1st column the row names

  #50 opened 3 years ago by KwatMDPhD
  2

• Plotting: Long gene set names not scaling properly in plot titles

  #49 opened 3 years ago by ACastanza
  5

• Consider making `compare` an independent command-line tool

  #51 opened 3 years ago by KwatMDPhD
  0

• Write out additional dict containing permuted enrichment scores for all sets

  #45 opened 3 years ago by ACastanza
  4

• Plotting: Flip Horizontal

  #37 opened 3 years ago by ACastanza
  1

• Embedded plotly CDN call-out in report links to "latest" tag instead of versioned

  #43 opened 3 years ago by ACastanza
  0

• Statistics: Sorting of tsvs appears Negative to Positive, reverse would be preferred

  #41 opened 3 years ago by ACastanza
  1

• Plotting: Annotate Maximum deviation from zero on plot

  #40 opened 3 years ago by ACastanza
  0

• Plotting: Change Hover Marker Color

  #39 opened 3 years ago by ACastanza
  4

• Plotting: 0.8.1 Enrichment Plots have "click to insert [x] title" text on HTML pages

  #48 opened 3 years ago by ACastanza
  1

• Rename `power` to be `exponent`

  #47 opened 3 years ago by KwatMDPhD
  0

• Plotting: Saving plot from the HTML as PNG uses generic name

  #38 opened 3 years ago by ACastanza
  1

• Error duplicated genes

  #36 opened 3 years ago by KwatMDPhD
  0

• Use full name for algorithm

  #46 opened 3 years ago by KwatMDPhD
  0

• List open-source contributors

  #35 opened 3 years ago by KwatMDPhD
  1

• Update significance calculations

  #42 opened 3 years ago by KwatMDPhD
  0

• Considering selecting sets in place

  #34 opened 3 years ago by KwatMDPhD
  0