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categoryCompare2 0.200.5

  • fixes getting statistics from gsea results, and actually has a test that it works.

categoryCompare2 0.200.4

  • fixes exporting annotation objects to JSON, in that every item should consistently be in a list array, and not a bare string when there is only a single annotated item.

categoryCompare2 0.200.3

  • adds the hypergeometric_features, gsea_features and binomial_features constructors as functions to make it easier to remember the arguments for the actual classes of the same names.

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.