TENxIO

DOI: 10.18129/B9.bioc.TENxIO  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see TENxIO.

Import methods for 10X Genomics files

Bioconductor version: 3.17

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]

Maintainer: Marcel Ramos <marcel.ramos at roswellpark.org>

Installation

To install this package, start R (version "4.3") 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")

 

HTML	R Script	TENxIO Quick Start Guide
PDF		Reference Manual
Text		NEWS

Details

biocViews	DataImport, Infrastructure, SingleCell, Software
Version	1.2.0
In Bioconductor since	BioC 3.16 (R-4.2) (1 year)
License	Artistic-2.0
Depends	R (>= 4.2.0), SingleCellExperiment, SummarizedExperiment
Imports	BiocBaseUtils, BiocGenerics, BiocIO, GenomeInfoDb, GenomicRanges, Matrix, MatrixGenerics, methods, RCurl, readr, R.utils, S4Vectors, utils
LinkingTo
Suggests	BiocStyle, DropletTestFiles, ExperimentHub, HDF5Array, knitr, RaggedExperiment, rhdf5, rmarkdown, Rsamtools, tinytest
SystemRequirements
Enhances
URL	https://github.com/waldronlab/TENxIO
BugReports	https://github.com/waldronlab/TENxIO/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	TENxIO_1.2.0.tar.gz
Windows Binary	TENxIO_1.2.0.zip
macOS Binary (x86_64)	TENxIO_1.2.0.tgz
macOS Binary (arm64)	TENxIO_1.2.0.tgz
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/
Package Downloads Report	Download Stats