BiocIO

DOI: 10.18129/B9.bioc.BiocIO  

Standard Input and Output for Bioconductor Packages

Bioconductor version: Release (3.17)

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 roswellpark.org>

Installation

To install this package, start R (version "4.3") 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")

 

HTML	R Script	BiocIO
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, DataImport, Software
Version	1.10.0
In Bioconductor since	BioC 3.12 (R-4.0) (3 years)
License	Artistic-2.0
Depends	R (>= 4.3.0)
Imports	BiocGenerics, S4Vectors, methods, tools
LinkingTo
Suggests	testthat, knitr, rmarkdown, BiocStyle
SystemRequirements
Enhances
URL
BugReports	https://github.com/Bioconductor/BiocIO/issues
Depends On Me	HelloRanges, LoomExperiment
Imports Me	BiocSet, extraChIPs, GenomicFeatures, HiCExperiment, HiContacts, HiCool, rtracklayer, TENxIO
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	BiocIO_1.10.0.tar.gz
Windows Binary	BiocIO_1.10.0.zip
macOS Binary (x86_64)	BiocIO_1.10.0.tgz
macOS Binary (arm64)	BiocIO_1.10.0.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
Old Source Packages for BioC 3.17	Source Archive