HelloRanges

This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see HelloRanges.

Introduce *Ranges to bedtools users

Bioconductor version: 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

Need some help? Ask on the Bioconductor Support site!

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

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 (64-bit only)

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/

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