BiocIO

DOI: 10.18129/B9.bioc.BiocIO    

This is the development version of BiocIO; for the stable release version, see BiocIO.

Standard Input and Output for Bioconductor Packages

Bioconductor version: Development (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>

Citation (from within R, enter citation("BiocIO")):

Installation

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

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.9.1
In Bioconductor since BioC 3.12 (R-4.0) (2 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 HelloRanges, LoomExperiment
Imports Me BiocSet, extraChIPs, GenomicFeatures, 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_1.9.1.tar.gz
Windows Binary BiocIO_1.9.1.zip
macOS Binary (x86_64) BiocIO_1.9.1.tgz
macOS Binary (arm64)
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

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