changes to gocats_2_annotation, checking for GO terms with no description, the actual base GO terms for each portion, and adding min and max arguments for the number of features annotated to a term.
categoryCompare2 0.100.30
adds documentation in the CLI vignette to using GSEA on the command line.
fixes filter_and_group.R to allow filtering of CLI GSEA results.
adds documentation in the CLI vignette about the JSON structure of each of the input files, both for hypergeometric testing and GSEA.
categoryCompare2 0.100.28
adds gene-set enrichment analysis (GSEA) to the command line interface. Note that this is only available by running run_enrichment.R directly. Currently, there is no way to modify the GSEA options, such as min_n and max_n.
categoryCompare2 0.100.25
adds gene-set enrichment analysis (GSEA) using the fgsea package. See gsea_features and gsea_feature_enrichment.
categoryCompare2 0.100.22
Fixed a bug where if nothing was significant, then all annotations were pulled into the graph.
categoryCompare2 0.100.21
Added more output in the binomial testing.
categoryCompare2 0.100.16
Fixing bugs around binomial testing.
categoryCompare2 0.100.9
Better importing of gocats objects.
categoryCompare2 0.100.8
Made it possible to do iterative filtering and grouping of the graph in the CLI.
categoryCompare2 0.100.7
Fixes to the CLI.
categoryCompare2 0.100.1
P-value adjustment is done by default.
categoryCompare2 0.99.161
Binomial enrichment.
categoryCompare2 0.99.160
Document finding communities in the vignettes.
categoryCompare2 0.99.159
CLI executables are available.
categoryCompare2 0.99.129
Really became the try inheritor to the original categoryCompare.