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