HelloRanges

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

Introduce *Ranges to bedtools users

Bioconductor version: Development (3.24)

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 <lawremi at gmail.com>

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

Seminal Bioconductor project articles:

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.

Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.

Installation

To install this package, start R (version "4.6") and enter:


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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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	1.39.0
In Bioconductor since	BioC 3.4 (R-3.3) (10 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), Seqinfo, SummarizedExperiment, BiocIO
Imports	docopt, stats, tools, utils
System Requirements
URL

Suggests	GenomeInfoDb, 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_1.39.0.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-arm64)
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