TENxIO
This is the development version of TENxIO; for the stable release version, see TENxIO.
Import methods for 10X Genomics files
Bioconductor version: Development (3.21)
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:
Maintainer: Marcel Ramos <marcel.ramos at sph.cuny.edu>
citation("TENxIO")):
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text |
Details
| biocViews | DataImport, Infrastructure, SingleCell, Software |
| Version | 1.9.3 |
| 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, 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 |
See More
| Suggests | BiocStyle, DropletTestFiles, ExperimentHub, knitr, RaggedExperiment(>= 1.29.5), rmarkdown, Rsamtools, tinytest |
| Linking To | |
| Enhances | |
| Depends On Me | VisiumIO |
| 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_1.9.3.tar.gz |
| Windows Binary (x86_64) | TENxIO_1.9.3.zip (64-bit only) |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/TENxIO |
| Source Repository (Developer Access) | git clone [email protected]:packages/TENxIO |
| Bioc Package Browser | https://code.bioconductor.org/browse/TENxIO/ |
| Package Short Url | https://bioconductor.org/packages/TENxIO/ |
| Package Downloads Report | Download Stats |