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>

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

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

Details

biocViews DataImport, Infrastructure, SingleCell, Software
Version 1.2.0
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
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
System Requirements
URL https://github.com/waldronlab/TENxIO
Bug Reports https://github.com/waldronlab/TENxIO/issues
See More
Suggests BiocStyle, DropletTestFiles, ExperimentHub, HDF5Array, knitr, RaggedExperiment, rhdf5, rmarkdown, Rsamtools, tinytest
Linking To
Enhances
Depends On Me
Imports Me
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Build Report 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
Old Source Packages for BioC 3.17 Source Archive