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OSCA-source / OSCA.advanced

Advanced steps of the OSCA book
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Revert fixes for non-legacy data in scRNAseq (#17) #18

Closed PeteHaitch closed 5 months ago

PeteHaitch commented 5 months ago

Aaron made changes to scRNAseq after I filed issues regarding the points raised in #17. So this PR:

  1. Bumps the minimum version of scRNAseq so reflect these fixes.
  2. Reverts most of the changes made in #17 (the change to more-hvgs.Rmd is still correct, so is not reverted).

The new minimal version of scRNAseq is not yet available from BiocManager::install() but should be in the next day or two. @lgeistlinger you may not want to merge this PR until the new version becomes available. Also, I have not bumped the version number of OSCA.advanced, so you will want to do that too before pushing to BioC's git.

PeteHaitch commented 5 months ago

@ltla Unfortunately the latest version of scRNAseq failed to build on BBS (https://bioconductor.org/checkResults/3.19/data-experiment-LATEST/scRNAseq/nebbiolo1-checksrc.html)

lgeistlinger commented 5 months ago

Thanks @PeteHaitch - just let me know once you'd like me to merge this one.

PeteHaitch commented 5 months ago

Good to merge now that scRNAseq v2.18.0 is available. You'll need to bump the OSCA.advanced version.

lgeistlinger commented 5 months ago

Thanks Pete. Merging.