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TENxIO

This is the development version of TENxIO; for the stable release version, see TENxIO.

Import methods for 10X Genomics files

Bioconductor version: Development (3.18)

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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.3.0
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
Linking To
Suggests BiocStyle, DropletTestFiles, ExperimentHub, HDF5Array, knitr, RaggedExperiment, rhdf5, rmarkdown, Rsamtools, tinytest
System Requirements
Enhances
URL https://github.com/waldronlab/TENxIO
Bug Reports https://github.com/waldronlab/TENxIO/issues
See More
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_1.3.0.tar.gz
Windows Binary TENxIO_1.3.0.zip
macOS Binary (x86_64)
macOS Binary (arm64) TENxIO_1.3.0.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