TENxIO
Import methods for 10X Genomics files
Bioconductor version: Release (3.19)
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("TENxIO")
):
Installation
To install this package, start R (version "4.4") 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 | ||
NEWS | Text |
Details
biocViews | DataImport, Infrastructure, SingleCell, Software |
Version | 1.6.1 |
In Bioconductor since | BioC 3.16 (R-4.2) (2 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 | VisiumIO |
Imports Me | |
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_1.6.1.tar.gz |
Windows Binary | TENxIO_1.6.1.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/ |
Package Downloads Report | Download Stats |
Old Source Packages for BioC 3.19 | Source Archive |