Importing scRNA-seq Data for Commandline QC
Source:vignettes/articles/cmd_import_scRNAseq_data_as_SCE.Rmd
cmd_import_scRNAseq_data_as_SCE.RmdSingle Cell ToolKit (SingleCellTK, SCTK) enables importing data from the following pre-processing tools-
- CellRanger
- Optimus
- DropEst
- BUStools
- Seqc
- STARSolo
- SingleCellExperiment object saved in RDS file
- AnnData object saved in HDF5 file
The following table describes how SCTK expects the inputs to be structured and passed for each import function. In all cases, SCTK retains the standard output directory structure from upstream tools. All the import functions return the imported counts matrix as an assay in a SingleCellExperiment object, with associated information in respective colData, rowData, reducedDims, and metadata fields.
Detailed information on function parameters and defaults are available in the Reference section. Please also refer to Commandline Quality Control documentation for the detail of other commandline input arguments.