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Published January 31, 2018 | Version v0.1.5
Software Open

hbc/bcbioRNASeq: bcbioRNASeq 0.1.5

Creators

  • 1. Harvard (@hbc)
  • 2. Harvard Chan School of Public Health
  • 3. Harvard School of Public Health

Description

  • Import shared dependency functions from bcbioBase instead of basejump.
  • Added method support for selectSamples().
  • organism and genomeBuild parameters are now user-definable in the main loadRNASeq() import function.
  • Fixed gene subsetting method on S4 object, which handles genes using intersect() in the featureCounts matrix.
  • Removed internal aggregateReplicates() code. This needs to be reworked and added back in a future release.
  • Improve method for handling a missing normalized counts matrix in the assays slot. This can occur when the user opts to skip the CPU-intensive DESeq2 normalizations.
  • Improved internal code for the quality control functions. Improved the if statements to be more class specific.
  • Renamed plotCorrelationHeatmap() transform argument to normalized, for consistency with the counts() generic.
  • Added title support to plots, where applicable.
  • Updated internal code for plotDEGHeatmap().
  • Updated internal marker handling code for plotGenderMarkers().
  • resulsTables() function now defaults to summary = TRUE.

Files

hbc/bcbioRNASeq-v0.1.5.zip

Files (5.9 MB)

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md5:f94866b5c9e906d164d7d31aafd7d697
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Additional details

Related works

Is supplement to
https://github.com/hbc/bcbioRNASeq/tree/v0.1.5 (URL)