Changes in version 0.200.9                       

  - added more tests to up the test coverage, and a test coverage badge.

                       Changes in version 0.200.8                       

  - fixes a long standing non-standard evaluation bug where if you tried
    to use an argument in a filtering operation, it would fail if it was
    within another function, or run in another process (#29).

                       Changes in version 0.200.7                       

  - fixes a bug where setting significant annotations where there was
    only a single enriched object in the combined object would return
    zero counts for enriched, which is not correct. Added test to verify
    the fix (#52).
  - fixes testing bugs where numbers of things would change due to
    changes in GO.db or the entrez annotation packages (#53).

                       Changes in version 0.200.6                       

  - implements a method for getting a statistical table for a single
    enriched_result.

                       Changes in version 0.200.5                       

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

                       Changes in version 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.

                       Changes in version 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
    (#49).

                       Changes in version 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 (#50).

                      Changes in version 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.

                      Changes in version 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.

                      Changes in version 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.

                      Changes in version 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.

                      Changes in version 0.100.25                       

  - adds gene-set enrichment analysis (GSEA) using the fgsea package.
    See gsea_features and gsea_feature_enrichment.

                      Changes in version 0.100.22                       

  - Fixed a bug where if nothing was significant, then all annotations
    were pulled into the graph.

                      Changes in version 0.100.21                       

  - Added more output in the binomial testing.

                      Changes in version 0.100.16                       

  - Fixing bugs around binomial testing.

                       Changes in version 0.100.9                       

  - Better importing of gocats objects.

                       Changes in version 0.100.8                       

  - Made it possible to do iterative filtering and grouping of the graph
    in the CLI.

                       Changes in version 0.100.7                       

  - Fixes to the CLI.

                       Changes in version 0.100.1                       

  - P-value adjustment is done by default.

                      Changes in version 0.99.161                       

  - Binomial enrichment.

                      Changes in version 0.99.160                       

  - Document finding communities in the vignettes.

                      Changes in version 0.99.159                       

  - CLI executables are available.

                      Changes in version 0.99.129                       

  - Really became the try inheritor to the original categoryCompare.