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scissors-analyses's Issues

Elyada lipid proc., secretory, & acinar gene lists

  • Lipid proc. vs (secretory, acinar, classical 1, classical 2, basal)
  • Secretory vs (lipid proc., acinar, classical 1, classical 2, basal)
  • Acinar vs. (lipid proc., secretory, classical 1, classical 2, basal)
  • Wilcoxon
  • L2FC > 0.25
  • adj. pvalue < 0.05
  • Filter highly expressed genes (90th percentile) from non-secretory, non-acinar, non-lipid proc., non-tumor in total cell pop.

Elyada tumor subclusters gene lists

  • basal vs. (classical 1 & classical 2)
  • classical 1 vs. (classical 2 & basal)
  • classical 2 vs. (classical 1 & basal)
  • basal vs. all classical
  • all classical vs. basal
  • Wilcoxon
  • L2FC > 0.25
  • Filter highly-expressed genes (90th percentile) from all non-tumor major celltypes

Elyada endothelial + perivascular gene lists

  • Endothelial vs. (perivascular, iCAF, myCAF, apCAF)
  • Perivascular vs. (endothelial, iCAF, myCAF, apCAF)
  • Wilcoxon
  • L2FC > 0.25
  • adj. pvalue < 0.05
  • Filter highly expressed genes (90th percentile) from non-perivascular, non-endothelial, non-CAF clusters in total cell pop.

Elyada major clusters gene list

  • One vs. rest
  • Wilcoxon
  • L2FC > 0.1
  • adj. pvalue < 0.05
  • Filter highly expressed genes (90th percentile) from all other clusters

Elyada CAF subclusters gene lists

  • apCAF vs. (iCAF + myCAF)
  • iCAF vs. (apCAF + myCAF)
  • myCAF vs. (apCAF + iCAF)
  • Wilcoxon
  • L2FC > 0.25
  • adj. pvalue < 0.05
  • Filter highly expressed genes (90th percentile) from all non-CAF clusters in total cell pop.

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