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HelloRanges

Introduce *Ranges to bedtools users


Bioconductor version: Release (3.18)

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 "4.3") and enter:


if (!require("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")
HelloRanges Tutorial PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Annotation, Coverage, DataImport, GenomeAnnotation, SequenceMatching, Sequencing, Software, VariantAnnotation
Version 1.28.0
In Bioconductor since BioC 3.4 (R-3.3) (7.5 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, BiocIO
Imports docopt, stats, tools, utils
System Requirements
URL
See More
Suggests HelloRangesData, BiocStyle, RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene
Linking To
Enhances
Depends On Me
Imports Me OMICsPCA
Suggests Me plyranges
Links To Me
Build Report Build Report

Package Archives

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

Source Package HelloRanges_1.28.0.tar.gz
Windows Binary HelloRanges_1.28.0.zip
macOS Binary (x86_64) HelloRanges_1.28.0.tgz
macOS Binary (arm64) HelloRanges_1.28.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/HelloRanges
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/HelloRanges
Bioc Package Browser https://code.bioconductor.org/browse/HelloRanges/
Package Short Url https://bioconductor.org/packages/HelloRanges/
Package Downloads Report Download Stats