modules

• cell_ranger
  • count

    Quantify gene expression in a single cell RNA-seq dataset.
  • mkref

    Creates an index for use with Cell Ranger. It can produce custom genomes if provided with the relevant (and correctly formatted) FastA and GTF files.
• 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.
• 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).
• R
  • biomaRt
    • get_mart

      Make a connection to the release-matched Ensembl database and saves the object as an RDS file.
  • GenomeInfoDB
    • convert_fai_to_seqinfo

      Converts a FastA index (`fai`) to a {GenomeInfoDb} `Seqinfo` object and saves the object to an RDS file.
  • GenomicRanges
    • convert_gtf_to_granges

      Reads a GTF file into a GRanges object and saves the object as an RDS file.
  • 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.
  • Signac
    • make_chromatin_assay

      Create a chromatin assay using Signac and a counts matrix.
• samtools
  • faidx

    Create a FastA index from a FastA file, providing a `.fai` file.
• 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.