TENxIO

This is the released version of TENxIO; for the devel version, see TENxIO.

Import methods for 10X Genomics files

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DOI: 10.18129/B9.bioc.TENxIO

Bioconductor version: Release (3.22)

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.

Author: Marcel Ramos [aut, cre] ORCID iD ORCID: 0000-0002-3242-0582

Maintainer: Marcel Ramos <marcel.ramos at sph.cuny.edu>

Citation (from within R, enter citation("TENxIO")):

Installation

To install this package, start R (version "4.5") and enter:


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

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("TENxIO")

TENxIO Quick Start Guide HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataImport, Infrastructure, SingleCell, Software

Version 1.12.0

In Bioconductor since BioC 3.16 (R-4.2) (3 years)

License Artistic-2.0

Depends R (>= 4.5.0), SingleCellExperiment, SummarizedExperiment

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

System Requirements

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

Bug Reports https://github.com/waldronlab/TENxIO/issues

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

Linking To

Enhances

Depends On Me VisiumIO, XeniumIO

Imports Me xenLite

Suggests Me

Links To Me

Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package TENxIO_1.12.0.tar.gz

Windows Binary (x86_64) TENxIO_1.12.0.zip

macOS Binary (x86_64)

macOS Binary (arm64)

Source Repository git clone https://git.bioconductor.org/packages/TENxIO

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/TENxIO

Bioc Package Browser https://code.bioconductor.org/browse/TENxIO/

Package Short Url https://bioconductor.org/packages/TENxIO/

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