TENxIO
This is the released version of TENxIO; for the devel version, see TENxIO.
Import methods for 10X Genomics files
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.14.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (4 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 | VisiumIO, XeniumIO |
| Imports Me | imageFeatureTCGA, 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_1.14.0.tar.gz |
| Windows Binary (x86_64) | TENxIO_1.14.0.zip |
| macOS Binary (big-sur-x86_64) | TENxIO_1.14.0.tgz |
| macOS Binary (sonoma-arm64) | TENxIO_1.14.0.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 |