Published November 27, 2023 | Version 1.4.0
Software Open

nf-core/differentialabundance: v1.4.0 - 2023-11-27

Creators

  • 1. DeepLife
  • 2. Boehringer Ingelheim
  • 3. University of Rostock
  • 4. Seqera Labs
  • 5. HKI Jena, MPI-EVA Leipzig

Description

This PR contains a particularly important fix in https://github.com/nf-core/differentialabundance/pull/20, which resolves a long-standing issue in proper usage of abundance values from the rnaseq workflow. Users can now take the lengths from that workflow (using rnaseq >=v3.13.2) and pass them to this workflow to account for transcript length biases across samples.

What's Changed

  • Post 1.3.1 release changes by @pinin4fjords in https://github.com/nf-core/differentialabundance/pull/186
  • Fix sample metadata table in the html report not paginating by @davidecarlson in https://github.com/nf-core/differentialabundance/pull/195
  • Fix GSEA indent in report by @WackerO in https://github.com/nf-core/differentialabundance/pull/190
  • Add optional scree plot to report by @WackerO in https://github.com/nf-core/differentialabundance/pull/192
  • Enable all genes for exploratory by @WackerO in https://github.com/nf-core/differentialabundance/pull/188
  • Add DESeq text to report by @WackerO in https://github.com/nf-core/differentialabundance/pull/193
  • Added colors to volcano by @WackerO in https://github.com/nf-core/differentialabundance/pull/194
  • Document correct RNAseq matrix usage by @pinin4fjords in https://github.com/nf-core/differentialabundance/pull/200
  • Update DESeq2/Limma by @WackerO in https://github.com/nf-core/differentialabundance/pull/201
  • Add design to report by @WackerO in https://github.com/nf-core/differentialabundance/pull/189
  • Transcript lengths for DESeq2 by @pinin4fjords in https://github.com/nf-core/differentialabundance/pull/203
  • Release v1.4.0 by @pinin4fjords in https://github.com/nf-core/differentialabundance/pull/204
  • V1.4.0 fixes by @pinin4fjords in https://github.com/nf-core/differentialabundance/pull/206
  • Dev -> master for v1.4.0 by @pinin4fjords in https://github.com/nf-core/differentialabundance/pull/205

New Contributors

  • @davidecarlson made their first contribution in https://github.com/nf-core/differentialabundance/pull/195

Full Changelog: https://github.com/nf-core/differentialabundance/compare/1.3.1...1.4.0

Files

nf-core/differentialabundance-1.4.0.zip

Files (5.5 MB)

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Additional details

Related works

Is supplement to
Software: https://github.com/nf-core/differentialabundance/tree/1.4.0 (URL)