HelloRanges

DOI: 10.18129/B9.bioc.HelloRanges    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see HelloRanges.

Introduce *Ranges to bedtools users

Bioconductor version: 3.9

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>

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

Installation

To install this package, start R (version "3.6") 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 1.10.0
In Bioconductor since BioC 3.4 (R-3.3) (3 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_1.10.0.tar.gz
Windows Binary HelloRanges_1.10.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) HelloRanges_1.10.0.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 https://bioconductor.org/packages/HelloRanges/
Package Downloads Report Download Stats

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