hbctraining/DGE_workshop_salmon_online

Issues

• update clustering figure from LRT lesson to reflect y axis change in new version

  #50 opened 3 months ago by hwick
  3

• LRT lesson refers to objects created in previous lessons which students may not have loaded up

  #51 opened 3 months ago by hwick
  1

• Formulas in self-learning broken

  #47 opened 3 months ago by Gammerdinger
  3

• Orgdb note didn't work in Gene annotation

  #53 opened 7 months ago by Gammerdinger
  2

• WGCNA link missing from lesson about network analysis

  #56 opened 4 months ago by hwick
  2

• updates to FA lessons

  #57 opened 6 months ago by mistrm82
  1

• featureCount link broken

  #54 opened 6 months ago by hwick
  1

• typos in LRT self learning and summarizing workflow

  #55 opened 7 months ago by hwick
  0

• Day 3 Exercises

  #52 opened 7 months ago by Gammerdinger
  0

• update FA lessons

  #49 opened 7 months ago by mistrm82
  0

• pathview doesn't work

  #45 opened 7 months ago by hwick
  2

• gseKEGG no longer recommends nperm, and other issues

  #44 opened 7 months ago by hwick
  2

• cnet plot size warning/legend, lesson text does not match plot output

  #48 opened 7 months ago by hwick
  1

• clustering coloring

  #39 opened a year ago by eberdan
  0

• count normalization figure

  #41 opened 7 months ago by eberdan
  1

• Broken Link

  #46 opened 7 months ago by benjibromberg
  1

• extra pink dot

  #38 opened 7 months ago by eberdan
  1

• Dispersion figure from DESEQ paper

  #42 opened a year ago by eberdan
  2

• deseq2 figure for wald test results

  #43 opened a year ago by eberdan
  0

• design formula order

  #40 opened a year ago by mistrm82
  4

• Add broken link

  #36 opened a year ago by jihe-liu
  1

• Bug Fixes

  #37 opened a year ago by Gammerdinger
  1

• create pull down descriptions for self-learning

  #31 opened 2 years ago by mistrm82
  0

• adda facet plot to link in viz lesson

  #34 opened 2 years ago by mistrm82
  0

• Creating annotation file tx2gene for NCBI human transcriptome

  #30 opened 2 years ago by ellalalalalalala
  1

• Adding gene names to KEGG output

  #26 opened 2 years ago by marypiper
  2

• for cluster profiler new msigdbr package

  #22 opened 2 years ago by marypiper
  2

• update the demo code at bottom of viz lesson

  #19 opened 2 years ago by mistrm82
  1

• Fix ggplot2 link

  #29 opened 3 years ago by Gammerdinger
  1

• a note for the warning in dotplot

  #16 opened 3 years ago by mistrm82
  3

• cleanup the workflow overview lesson

  #17 opened 3 years ago by mistrm82
  1

• paring down the dispersion lesson

  #15 opened 3 years ago by mistrm82
  1

• GSEgo error

  #18 opened 3 years ago by mistrm82
  3

• apeglm stat removed

  #25 opened 3 years ago by marypiper
  2

• Look into this package for GO term hierarchy viz

  #20 opened 3 years ago by marypiper
  1

• Add note about knockout genes continuing to be expressed

  #21 opened 3 years ago by rkhetani
  2

• Create project with data and folders

  #23 opened 3 years ago by jihe-liu
  1

• clusterProfiler for gene lists split by expression change

  #3 opened 4 years ago by mistrm82
  1

• update lfcShrink for apeglm

  #4 opened 4 years ago by mistrm82
  0

• update heatmap image

  #2 opened 4 years ago by mistrm82
  1