GUDMAP/RBK scRNA-Seq Image Generation Pipeline

Introduction

To Run:

• Available parameters:
  • --rda R datafile
  • --seurat name of Seurat object in R datafile
  • --tsne true/false if tSNE calculated in Seurat object
  • --umap true/false if UMAP calculated in Seurat object
  • --assay name of assay in Seurat object to use for expression
  • --slot name of slot in Seurat object to use for expression
  • --scale true/false if assay needs scaling in Seurat object for expression
  • --sample number of cells to downsample Seurat object (0 for no downsampling)
  • --groups .csv file with a list of identity groups (1 pdf line) to output images for in Seurat object
  • --convert reference used in Seurat object for conversion to NCBI ID ("NO" for no conversion), must have a conversion file named *.to.NCBI.txt in .workflow/files to work
  • --outDir optional output directiory location
• FULL EXAMPLE:

  nextflow run workflow/scrna-seg_imgen.nf --rda ./data/sc10x.R --seurat sc10x --tsne true --umap false --assay RNA --slot scale.data --scale true --sample 0 --groups ./data/groups.csv --convert GRCh38p5

• Processes
  • createMatrix
    • Inputs:
      • R datafile
      • Seurat object name
      • Calculate tSNE?
      • Calculate UMAP?
      • Seurat assay
      • Seurat slot
      • Scale?
      • Number of cells to sample to
    • Outputs:
      • Raw matrix file (similar to 10x Genomics output)
  • createGroups
    • Inputs:
      • R datafile
      • Seurat object name
      • Groups to use
      • Downsampled cell barcodes
    • Outputs:
      • Files with cell barcodes and identities
  • renameGenes
    • Inputs:
      • Raw matrix files
      • Reference genome to convert
      • NCBI ID conversion file
    • Outputs:
      • Final matrix files
  • plotIdentGroup
    • Inputs:
      • Final matrix files
      • Identity groups
      • Calculate tSNE?
      • Calculate UMAP?
    • Outputs:
      • Image Group plots
  • plotFeatures
    • Inputs:
      • Final matrix
      • Chunked genes (1000 genes per chunk)
      • Calculate tSNE?
      • Calculate UMAP?
    • Outputs:
      • Feature plots
  • plotViolinBox
    • Inputs:
      • Final matrix
      • Chunked genes (1000 genes per chunk)
      • Identity groups
      • Identity group lists
    • Output:
      • Violin Box plot

CHANGELOG

Credits

This worklow is was developed by Bioinformatic Core Facility (BICF), Department of Bioinformatics

PI

Venkat S. Malladi
Faculty Associate & Director
Bioinformatics Core Facility
UT Southwestern Medical Center
orcid.org/0000-0002-0144-0564
venkat.malladi@utsouthwestern.edu

AND

Douglas W. Strand
Assistant Professor
Department of Urology
UT Southwestern Medical Center
orcid.org/0000-0002-0746-927X
douglas.strand@utsouthwestern.edu

Developers

Gervaise H. Henry
Computational Biologist
Department of Urology
UT Southwestern Medical Center
orcid.org/0000-0001-7772-9578
gervaise.henry@utsouthwestern.edu