BiocIO
This is the released version of BiocIO; for the devel version, see BiocIO.
Standard Input and Output for Bioconductor Packages
Bioconductor version: Release (3.20)
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")):
Installation
To install this package, start R (version "4.4") 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 | 1.16.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (4.5 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 | BiocSet, BSgenomeForge, extraChIPs, HiCExperiment, HiContacts, HiCool, rtracklayer, TENxIO, tidyCoverage, txdbmaker, VisiumIO |
| 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_1.16.0.tar.gz |
| Windows Binary (x86_64) | BiocIO_1.16.0.zip |
| macOS Binary (x86_64) | BiocIO_1.16.0.tgz |
| macOS Binary (arm64) | BiocIO_1.16.0.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 |