workflows

• genome_preparation

  These processes can be executed independently of datassets, their parameters do not depend on the data but on the genome used in the analysis.
• quantification

  A variety of methods are implemented that can take FastQ files and output quantified expression data, creating intermediate files such as indexes as required.

  • cell_ranger

    Use the 10X `cellranger` software to quantify expression and optionally create a genome index against which gene expression can be quantified.
  • cell_ranger_arc

    Using `cellranger-arc` software, libraries for snRNA-seq and cell-matched snATAC-seq assays are quantified against an index, which can be optionally created.
  • cell_ranger_multi

    Using `cellranger-multi` software, barcoded and probe-based libraries for gene expression assays are quantified against an index, which can be optionally created.
• seurat

  Analysis of single cell data using Seurat-based methods.

  • prepare
    • cell_ranger

      Using the filtered single cell expression matrix, output from Cell Ranger, a Seurat object is prepared with little modification.
    • cell_ranger_arc

      Using the filtered single nucleus expression and accessibility matrices, written by Cell Ranger ARC, a Seurat object is prepared that contains RNA and chromatin accessibility assays with little modification.