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Version 3 Update #6

Merged
merged 16 commits into from
Jan 9, 2025
Merged

Version 3 Update #6

merged 16 commits into from
Jan 9, 2025

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chenv3
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@chenv3 chenv3 commented Jan 9, 2025

  • Added in a force cells 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

@chenv3 chenv3 merged commit 6aaefe4 into main Jan 9, 2025
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@chenv3 chenv3 deleted the dev branch January 9, 2025 22:46
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