NEWS.md

In rmflight/categoryCompare2: Meta-Analysis of High-Throughput Experiments Using Feature Annotations

categoryCompare2 0.200.2

• changes hypergeom_features to hypergeometric_features.
• because the hypergeometrc_features necessitates changes to actual code written by any users, I bumped the version from 0.100 to 0.200.
• implements hypergeometric_result, gsea_result, and binomial_result as more specific classes of enrichemnt_result, which makes all of the combining and filtering work for everything.
• made the vignettes use pre-processed data so that there won't be any issues from the affy package and segfaults.

categoryCompare2 0.100.32

• changes binomial_feature_enrichment min_features to 6, as anything under this is not likely to be useful for binomial testing.
• fixes some failing tests.
• adds ability to use combine_enrichments on binomial_enriched objects.

categoryCompare2 0.100.31

• 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.

rmflight/categoryCompare2 documentation built on July 16, 2025, 2:48 p.m.