modules
- cell_ranger
- cell_ranger_arc
- count
Aligns and quantifies FastQ files from a 10X snRNA+ATAC-seq experiment against a reference genome. Output matrices are provided in triplet and h5 formats.
- make_libraries_csv
Creates a sample sheet for a whole project, listing the sample names, assay types and paths to FastQ files. It can be subset to produce a sample sheet for a sample.
- mkref
Creates an index for use with Cell Ranger ARC. It can produce custom genomes if provided with the relevant (and correctly formatted) FastA and GTF files.
- count
- cell_ranger_multi
- count
Aligns and quantifies FastQ files from a multiomic 10x experiment against a reference genome and include VDJ-B/T and cell surface markers. Output matrices for gene expression and features are provided in triplet and h5 formats. VDJ data are provided separately.
- make_input_csv
Creates a configuration file for a library, listing the sample names, assay types and paths to FastQ files (etc).
- count
- R
- biomaRt
- get_mart
Make a connection to the release-matched Ensembl database and saves the object as an RDS file.
- get_mart
- GenomeInfoDB
- convert_fai_to_seqinfo
Converts a FastA index (`fai`) to a {GenomeInfoDb} `Seqinfo` object and saves the object to an RDS file.
- convert_fai_to_seqinfo
- GenomicRanges
- convert_gtf_to_granges
Reads a GTF file into a GRanges object and saves the object as an RDS file.
- convert_gtf_to_granges
- Seurat
- make_assay
Writes assay objects as RDS files for a specified assay type.
- make_object
A Seurat object is created from the assays, metadata and miscellaneous objects and written to an RDS file.
- percentage_feature_set
Adds a metadata variable that shows the perentage of a cell's data that originates from features that match a regex.
- write_10x_counts_matrices
Reads a directory containing Cell Ranger-formatted output into a list of matrices.
- make_assay
- Signac
- make_chromatin_assay
Create a chromatin assay using Signac and a counts matrix.
- make_chromatin_assay
- biomaRt
- samtools
- faidx
Create a FastA index from a FastA file, providing a `.fai` file.
- faidx
- tools
- cat
Concatenate multiple files into a single output file. Different input formats can be used; based on the extension, YAML files are concatenated using `yq`, otherwise `cat` is used.
- cat