# sparrow 1.14

## Enhancements

* Updated to support refactored msigdbr package (version >= 10.0.0), which now
  only includse the human Hallmark genesets internally. The msigdbr package
  relies on an external (non CRAN) msigdbdf package, for the rest of the
  (now more recent) definitions of the MSigDB gene set collections.

## Enhancements

* The default "zero-centering" logic is updated in mgheatmap2 when `col` isn't
  specified, but `recenter` is (backported to release 3.14)

## Bug Fixes

* `calculateIndividualLogFC` is updated to handle situations when `$genes`
  data.frame has column names that collide with statistics generated from
  differential expression, like `pval`, `padg`, and `AveExpr`. Thanks to
  @sandersen12 for the bug report.

# sparrow 1.0 (2021-10-XX)

## Enhancements

* Released to Bioconductor
* Adds support for use of BiocSet as a means by which users can bring their
  genesets to -- or take them from -- sparrow.
* Improvements to the corplot() functionality contributed by by Arkadiusz Gladki
  (@gladki). Users can specify the size of the text reported in the bottom half
  of the pair plot, and spurious/annoying warnings that were produced after a
  a totally valid call are no longer produced.

## Breaking Changes from Pre-release

* First two parameters in ora() function have been swapped so that the
  first parameter (`x`) is the object (data.frame) to run an over
  representation analysis against, and the second parameter is the GeneSetDb.
* scoreSingleSamples no longer drops features in `y` that are not found
  in the GeneSetDb used for scoring. This was changed so that gsva and ssGSEA
  scores match the scores produced by a normal GSVA::gsva call. You can set
  the `drop.unconformed = TRUE` to retain the older behavior.
