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.
- cell_ranger
- 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.
- cell_ranger
- prepare