TENxIO: A Bioconductor package for importing 10X Genomics files

The package provides file classes based on BiocIO for common file extensions found in the 10X Genomics website.

Supported file types

Here is a table of supported file and file extensions and their imported classes:

Extension	Class	Imported as
.h5	TENxH5	SingleCellExperiment w/ TENxMatrix
.mtx / .mtx.gz	TENxMTX	SummarizedExperiment w/ dgCMatrix
.tar.gz	TENxFileList	SingleCellExperiment w/ dgCMatrix
peak_annotation.tsv	TENxPeaks	GRanges
fragments.tsv.gz	TENxFragments	RaggedExperiment
.tsv / .tsv.gz	TENxTSV	tibble

See also

Useful links:

• https://github.com/waldronlab/TENxIO

• Report bugs at https://github.com/waldronlab/TENxIO/issues

Author

Maintainer: Marcel Ramos marcel.ramos@sph.cuny.edu (ORCID)