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2.2 - Avenue of Poplars

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@WackerO WackerO released this 21 Aug 08:44
· 165 commits to master since this release
2.2
f5e54b6
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Learn about vigilant mode.

Added

  • #215 Added gene_name to boxplot titles and filenames; increased threshold before overlapping PCA labels are hidden
  • #213 Added smrnaseq input support
  • #212 Added computational methods if no --software_versions
  • #206 Added logic to decide between rlog and vst, added tryCatch for heatmap saving because this only works unreliably
  • #202 Added background list to pathway analysis
  • #197 Added gprofiler version string to report
  • #196 Added optional --quote parameter

Changed

  • #219 Release 2.2 to master
  • #220 Commit suggestions from PR review for release 2.2
  • #218 Preparing release 2.2 with version bumps
  • #217 For rsem/salmon-imports, when a GTF is sometimes missing gene_names, these are now replaced by gene_ids instead
  • #215 Boxplots of genes are now generated from rlog/vst counts instead of raw counts. Also, if batch effect correction is enabled, boxplots will be generated before and after correction
  • #214 Added smrnaseq input support -->follow-up to check that the CI test works. Modified smrnaseq testdata to be like QBiC datasets. Updated container env and fixed a resulting bug with include_graphics. Heatmaps are now equally ordered in zip and report
  • #211 Replaced heatmaply with pheatmap for static plots and removed kaleido and reticulate from container
  • #209 Template update to 2.9, Chromium Falcon; exchanged file.exists for nf-core validation checks; changed round_DE param to int
  • #206 Changed < and > to <= and => for logF/pval comparisons, renamed gene_counts_tables/deseq2_library_scaled_gene_counts.tsv to deseq2_library_scaled_gene_counts.tsv and added entry to the folder explanation; renamed param pval_threshold to adj_pval_threshold
  • #205 Template update
  • #204 Changed relevel path in test_relevel.config to the qbic-pipelines repo
  • #203 Switched from Dockerhub to GHCR
  • #200 Made software_versions optional
  • #198 Changed heatmaps to scale in size automatically

Fixed

  • #212 Fixed movability of interactive gostplots
  • #208 Fixed relevel bug, the function should now finally work!
  • #207 Fixed check of samples in counts vs metadata
  • #206 Added correct plot titles to meanSdPlot (depending on normalization)
  • #195 Fixed section error in report
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