TENxIO
This is the development version of TENxIO; for the stable release version, see TENxIO.
Import methods for 10X Genomics files
Bioconductor version: Development (3.24)
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]
, NCI [fnd] (GrantNo.: U24CA289073)
Maintainer: Marcel Ramos <marcel.ramos at sph.cuny.edu>
citation("TENxIO")):
Installation
To install this package, start R (version "4.6") 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
| Reference Manual |
Details
| biocViews | DataImport, Infrastructure, SingleCell, Software |
| Version | 1.15.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (3.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.5.0), SingleCellExperiment, SummarizedExperiment |
| Imports | BiocBaseUtils, BiocGenerics, BiocIO, Seqinfo, GenomicRanges, HDF5Array, Matrix, MatrixGenerics, methods, 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(>= 1.33.3), rmarkdown, Rsamtools, tinytest |
| Linking To | |
| Enhances | |
| Depends On Me | |
| 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 | |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (big-sur-arm64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/TENxIO |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/TENxIO |
| Package Short Url | https://bioconductor.org/packages/TENxIO/ |
| Package Downloads Report | Download Stats |