HelloRanges

DOI: 10.18129/B9.bioc.HelloRanges    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see HelloRanges.

Introduce *Ranges to bedtools users

Bioconductor version: 3.8

Translates bedtools command-line invocations to R code calling functions from the Bioconductor *Ranges infrastructure. This is intended to educate novice Bioconductor users and to compare the syntax and semantics of the two frameworks.

Author: Michael Lawrence

Maintainer: Michael Lawrence <michafla at gene.com>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("HelloRanges")

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("HelloRanges")

 

PDF	R Script	HelloRanges Tutorial
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, Coverage, DataImport, GenomeAnnotation, SequenceMatching, Sequencing, Software, VariantAnnotation
Version	1.8.0
In Bioconductor since	BioC 3.4 (R-3.3) (2.5 years)
License	GPL (>= 2)
Depends	methods, BiocGenerics, S4Vectors(>= 0.17.39), IRanges(>= 2.13.12), GenomicRanges(>= 1.31.10), Biostrings(>= 2.41.3), BSgenome, GenomicFeatures(>= 1.31.5), VariantAnnotation(>= 1.19.3), Rsamtools, GenomicAlignments(>= 1.15.7), rtracklayer(>= 1.33.8), GenomeInfoDb, SummarizedExperiment
Imports	docopt, stats, tools, utils
LinkingTo
Suggests	HelloRangesData, BiocStyle
SystemRequirements
Enhances
URL
Depends On Me
Imports Me	OMICsPCA
Suggests Me	plyranges
Links To Me
Build Report

Package Archives

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

Source Package	HelloRanges_1.8.0.tar.gz
Windows Binary	HelloRanges_1.8.0.zip
Mac OS X 10.11 (El Capitan)	HelloRanges_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/HelloRanges
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/HelloRanges
Package Short Url	http://bioconductor.org/packages/HelloRanges/
Package Downloads Report	Download Stats