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TENxIO

Import methods for 10X Genomics files

Bioconductor version: 3.24 · Package version: 1.15.0

Provides a structured S4 approach to importing data files from the 10X pipelines. It mainly supports Single Cell Multiome ATAC + Gene Expression data among other data types. The main Bioconductor data representations used are SingleCellExperiment and RaggedExperiment.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("TENxIO")

Details

MaintainerMarcel Ramos <marcel.ramos@sph.cuny.edu>
AuthorMarcel Ramos [aut, cre] (ORCID: <https://orcid.org/0000-0002-3242-0582>), NCI [fnd] (GrantNo.: U24CA289073)
LicenseArtistic-2.0
URLhttps://github.com/waldronlab/TENxIO
Bug Reportshttps://github.com/waldronlab/TENxIO/issues
Downloads rank561
Source branchdevel
biocViewsDataImport, Infrastructure, SingleCell, Software

Documentation

Download

Follow the installation instructions to use this package in your R session.

Source packageTENxIO_1.15.0.tar.gz
Windows binary (x86_64)TENxIO_1.15.0.zip
macOS binary (arm64)TENxIO_1.15.0.tgz
macOS binary (x86_64)TENxIO_1.15.0.tgz
Dependencies

Depends: R (>= 4.5.0), SingleCellExperiment, SummarizedExperiment

Imports: BiocBaseUtils, BiocGenerics, BiocIO, Seqinfo, GenomicRanges, HDF5Array, Matrix, MatrixGenerics, methods, readr, rhdf5, R.utils, S4Vectors, utils

Suggests: BiocStyle, DropletTestFiles, ExperimentHub, knitr, RaggedExperiment (>= 1.33.3), rmarkdown, Rsamtools, tinytest

Reverse dependencies

Depends On Me (2): VisiumIO, XeniumIO

Imports Me (2): imageFeatureTCGA, xenLite

Suggests Me (1): GEOquery