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.