BiocIO

DOI: 10.18129/B9.bioc.BiocIO    

Standard Input and Output for Bioconductor Packages

Bioconductor version: Release (3.14)

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], Bioconductor Package Maintainer [cre]

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

Installation

To install this package, start R (version "4.1") 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

Details

biocViews	Annotation, DataImport, Software
Version	1.4.0
In Bioconductor since	BioC 3.12 (R-4.0) (1.5 years)
License	Artistic-2.0
Depends	R (>= 4.0)
Imports	BiocGenerics, S4Vectors, methods, tools
LinkingTo
Suggests	testthat, knitr, rmarkdown, BiocStyle
SystemRequirements
Enhances
URL
BugReports	https://github.com/Bioconductor/BiocIO/issues
Depends On Me	LoomExperiment
Imports Me	BiocSet, GenomicFeatures, rtracklayer
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	BiocIO_1.4.0.tar.gz
Windows Binary	BiocIO_1.4.0.zip
macOS 10.13 (High Sierra)	BiocIO_1.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/BiocIO
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BiocIO
Package Short Url	https://bioconductor.org/packages/BiocIO/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.14	Source Archive