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alabaster.files

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

Wrappers to Save Common File Formats


Bioconductor version: Development (3.19)

Save common bioinformatics file formats within the alabaster framework. This includes BAM, BED, VCF, bigWig, bigBed, FASTQ, FASTA and so on. We save and load additional metadata for each file, and we support linkage between each file and its corresponding index.

Author: Aaron Lun [aut, cre]

Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>

Citation (from within R, enter citation("alabaster.files")):

Installation

To install this package, start R (version "4.4") and enter:


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

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

BiocManager::install("alabaster.files")

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("alabaster.files")
Saving common file formats HTML R Script
Reference Manual PDF

Details

biocViews DataImport, DataRepresentation, Software
Version 1.1.1
In Bioconductor since BioC 3.18 (R-4.3) (< 6 months)
License MIT + file LICENSE
Depends alabaster.base
Imports methods, S4Vectors, BiocGenerics, Rsamtools
System Requirements
URL
See More
Suggests BiocStyle, rmarkdown, knitr, testthat, VariantAnnotation, rtracklayer, Biostrings
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package alabaster.files_1.1.1.tar.gz
Windows Binary
macOS Binary (x86_64) alabaster.files_1.1.1.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/alabaster.files
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/alabaster.files
Bioc Package Browser https://code.bioconductor.org/browse/alabaster.files/
Package Short Url https://bioconductor.org/packages/alabaster.files/
Package Downloads Report Download Stats