Issues

• add gsea and binomial enrichment to the vignette

  MoseleyBioinformaticsLab/categoryCompare2#48 · Filter by author rmflight opened on Jul 3, 2025
  

• fix vignettes and cli code

  MoseleyBioinformaticsLab/categoryCompare2#47 · Filter by author rmflight opened on Jul 3, 2025
  

• Inconsistent data type values in annotations.json

  MoseleyBioinformaticsLab/categoryCompare2#26 · Filter by author ehinderer opened on Nov 13, 2018
  1

• Need more informative error on missing json_file when running categoryCompare.R executable

  MoseleyBioinformaticsLab/categoryCompare2#24 · Filter by author ehinderer opened on Mar 11, 2018
  

• wrapper for most common use case

  MoseleyBioinformaticsLab/categoryCompare2#23 · Filter by author rmflight opened on Apr 23, 2017

• consider R6 methods

  MoseleyBioinformaticsLab/categoryCompare2#22 · Filter by author rmflight opened on Aug 25, 2016

• add default labels, and methods to change them

  MoseleyBioinformaticsLab/categoryCompare2#21 · Filter by author rmflight opened on Aug 25, 2016
  1

• move generate_annotation_similarity_graph switch outside the calc_similarity

  MoseleyBioinformaticsLab/categoryCompare2#20 · Filter by author rmflight opened on May 14, 2016

• add weight based on enrichment similarity

  MoseleyBioinformaticsLab/categoryCompare2#19 · Filter by author rmflight opened on Apr 26, 2016

• hypergeom_feature constructor

  MoseleyBioinformaticsLab/categoryCompare2#17 · Filter by author rmflight opened on Apr 26, 2016

• hypergeom_feature should create universe if null

  MoseleyBioinformaticsLab/categoryCompare2#16 · Filter by author rmflight opened on Apr 26, 2016

• single function for generating annotation object from eg.db

  MoseleyBioinformaticsLab/categoryCompare2#15 · Filter by author rmflight opened on Apr 26, 2016

• vignette should show eg.db usage

  MoseleyBioinformaticsLab/categoryCompare2#14 · Filter by author rmflight opened on Apr 26, 2016

• more testing!

  MoseleyBioinformaticsLab/categoryCompare2#13 · Filter by author rmflight opened on Jun 17, 2015

• use Map to do multiple hypergeometric or GSEA enrichment

  vignette
  MoseleyBioinformaticsLab/categoryCompare2#10 · Filter by author rmflight opened on May 29, 2015 · v1.0, bioc 3.2
  

• converting from v1 to v2 code

  vignette
  MoseleyBioinformaticsLab/categoryCompare2#9 · Filter by author rmflight opened on May 29, 2015 · v1.0, bioc 3.2
  

• have example with different gene universes

  vignette
  MoseleyBioinformaticsLab/categoryCompare2#8 · Filter by author rmflight opened on May 29, 2015 · v1.0, bioc 3.2
  

• convert Category result objects to enrichment_objects

  core
  MoseleyBioinformaticsLab/categoryCompare2#6 · Filter by author rmflight opened on May 29, 2015 · v1.0, bioc 3.2
  

• annotation_combinations should take a logical matrix

  coreenhancement
  MoseleyBioinformaticsLab/categoryCompare2#5 · Filter by author rmflight opened on May 29, 2015 · v1.0, bioc 3.2
  

• set individual cutoffs

  coreenhancement
  MoseleyBioinformaticsLab/categoryCompare2#4 · Filter by author rmflight opened on May 29, 2015 · v1.0, bioc 3.2