TENxIO
This is thereleased version of TENxIO; for the devel version, seeTENxIO.
Import methods for 10X Genomics files
Bioconductor version: Release (3.22)
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: 0000-0002-3242-0582
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")BiocManager::install("TENxIO")For older versions of R, please refer to the appropriateBioconductor 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 | 1.12.1 |
| In Bioconductor since | BioC 3.16 (R-4.2) (3 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.5.0),SingleCellExperiment,SummarizedExperiment |
| Imports | BiocBaseUtils,BiocGenerics,BiocIO,Seqinfo,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(>= 1.33.3),rmarkdown,Rsamtools,tinytest |
| Linking To | |
| Enhances | |
| Depends On Me | VisiumIO,XeniumIO |
| Imports Me | xenLite |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | TENxIO_1.12.1.tar.gz |
| Windows Binary (x86_64) | TENxIO_1.12.0.zip |
| macOS Binary (x86_64) | TENxIO_1.12.1.tgz |
| macOS Binary (arm64) | TENxIO_1.12.1.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 3.22 | Source Archive |