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.