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v3.0.0

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@chenv3 chenv3 released this 09 Jan 22:53
· 84 commits to main since this release
v3.0.0
6aaefe4
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Learn about vigilant mode.

What's Changed

  • Version 3 Update by @chenv3 in #6
    • Added --forcecells flag which can be applied to the following pipelines
      • GEX
      • CITE
      • MULTI
      • ATAC
    • Added support for additional version to --cellranger flag for GEX, CITE, VDJ, and MULTi pielines
      • Also handles version 9.0.0
    • Added support for running pipeline on Cell Ranger output
    • Changed cellranger calls so optional flags are on the same line as the last required flag
    • Edits to GEX pipeline
      • Changed to running Seurat v5 using R4.4.0
      • Set an upper limit of 100 for mitochondrial filter threshold
      • Added in Seurat integration for normalization and SCTransform. Runs if more than one sample is processed
        • CCA
        • Joint PCA
        • RPCA
        • Harmony
      • Create a summary integration report
    • Edits to CITE pipeline
      • Add basic Seurat QC analysis
        • If hashtags are run with the name starting with “HTO-” or “HTO_‘, will try to run hashtag demultiplexing

Full Changelog: v2.0.1...v3.0.0

Contributors

chenv3
Assets 2
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