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Analysis pipeline for CRC patient samples

The preprocessing pipeline for scRNA-seq has four modules consisting of parameterized Rmarkdown scripts:

  1. QC+filtering: prepro_01_qc.Rmd
    • takes velocyto.loom file and creates seu_raw object (assumes path: "_data/_patients/velocyto/p007n.loom")
    • needs filtering parameters for qc (e.g. mito reads)
  2. Subsampling: prepro_02_sub.Rmd
    • takes a Seurat object as input file and outputs a Seurat object as output with N cells
  3. Anchoring: prepro_03_anchoring.Rmd
    • takes multiple qc-filtered Seurat objects and merges (and anchors) them into one merged (and one anchored) Seurat object
  4. Annotation: prepro_04_ann.Rmd
    • takes a seurat object and annotates it with preliminary cell type information and gene expression signatures

Wrapper functions for module calls are described in prepro_00.R. All calls are listed in prepro.sh. R library dependencies are listed within each module file.

After preprocessing, figures were generated as described in scCRC_paper_figures.Rmd.

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