BiocIO
This is the released version of BiocIO; for the devel version, see BiocIO.
Standard Input and Output for Bioconductor Packages
Bioconductor version: Release (3.23)
The `BiocIO` package contains high-level abstract classes and generics used by developers to build IO funcionality within the Bioconductor suite of packages. Implements `import()` and `export()` standard generics for importing and exporting biological data formats. `import()` supports whole-file as well as chunk-wise iterative import. The `import()` interface optionally provides a standard mechanism for 'lazy' access via `filter()` (on row or element-like components of the file resource), `select()` (on column-like components of the file resource) and `collect()`. The `import()` interface optionally provides transparent access to remote (e.g. via https) as well as local access. Developers can register a file extension, e.g., `.loom` for dispatch from character-based URIs to specific `import()` / `export()` methods based on classes representing file types, e.g., `LoomFile()`.
Author: Martin Morgan [aut], Michael Lawrence [aut], Daniel Van Twisk [aut], Marcel Ramos [cre]
Maintainer: Marcel Ramos <marcel.ramos at sph.cuny.edu>
citation("BiocIO")):
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("BiocIO")
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("BiocIO")| BiocIO | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, DataImport, Software |
| Version | 1.22.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.3.0) |
| Imports | BiocGenerics, S4Vectors, methods, tools |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/Bioconductor/BiocIO/issues |
See More
| Suggests | testthat, knitr, rmarkdown, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | BSgenome, HelloRanges, LoomExperiment |
| Imports Me | Bioc.gff, BiocSet, BSgenomeForge, gmapR, HiCExperiment, HiContacts, HiCool, imageFeatureTCGA, rtracklayer, TENxIO, tidyCoverage, txdbmaker, VisiumIO, XeniumIO |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | BiocIO_1.22.0.tar.gz |
| Windows Binary (x86_64) | BiocIO_1.22.0.zip |
| macOS Binary (big-sur-x86_64) | BiocIO_1.22.0.tgz |
| macOS Binary (sonoma-arm64) | BiocIO_1.22.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/BiocIO |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/BiocIO |
| Bioc Package Browser | https://code.bioconductor.org/browse/BiocIO/ |
| Package Short Url | https://bioconductor.org/packages/BiocIO/ |
| Package Downloads Report | Download Stats |