plyranges

This is the released version of plyranges; for the devel version, see plyranges.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7

A fluent interface for manipulating GenomicRanges

Bioconductor version: Release (3.23)

A dplyr-like interface for interacting with the common Bioconductor classes Ranges and GenomicRanges. By providing a grammatical and consistent way of manipulating these classes their accessiblity for new Bioconductor users is hopefully increased.

Author: Stuart Lee [aut] ORCID: 0000-0003-1179-8436 , Michael Lawrence [aut, ctb], Dianne Cook [aut, ctb], Spencer Nystrom [ctb] ORCID: 0000-0003-1000-1579 , Pierre-Paul Axisa [ctb], Michael Love [ctb, cre]

Maintainer: Michael Love <michaelisaiahlove at gmail.com>

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

Stuart Lee, Michael Lawrence, Dianne Cook. plyranges: A fluent interface for manipulating GenomicRanges. doi:10.18129/B9.bioc.plyranges, R package version 1.32.0, https://bioconductor.org/packages/plyranges.

Generated from the package metadata; it may differ from the package's own citation.

Installation

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

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

BiocManager::install("plyranges")

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("plyranges")

Introduction	HTML	R Script
Additional examples of plyranges	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Coverage, DataRepresentation, Infrastructure, Software, WorkflowStep
Version	1.32.0
In Bioconductor since	BioC 3.7 (R-3.5) (8.5 years)
License	Artistic-2.0
Depends	R (>= 3.5), BiocGenerics, IRanges (>= 2.12.0), GenomicRanges (>= 1.28.4), dplyr
Imports	methods, rlang (>= 0.2.0), magrittr, tidyselect (>= 1.0.0), rtracklayer, GenomicAlignments, Seqinfo, Rsamtools, S4Vectors (>= 0.23.10), utils
System Requirements
URL	https://tidyomics.github.io/plyranges
Bug Reports	https://github.com/tidyomics/plyranges

Suggests	knitr, BiocStyle, rmarkdown, testthat (>= 2.1.0), HelloRanges, HelloRangesData, BSgenome.Hsapiens.UCSC.hg19, pasillaBamSubset, covr, ggplot2
Linking To
Enhances
Depends On Me	plyinteractions
Imports Me	BOBaFIT, BUSpaRse, cfDNAPro, Damsel, fluentGenomics, GenomicCoordinates, GenomicPlot, InPAS, katdetectr, multicrispr, MutSeqR, nullranges, plotgardener, profileplyr, splicelogic, tidyomics
Suggests Me	EpiCompare, extraChIPs, memes, rigvf, svaNUMT, svaRetro, tidyCoverage
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	plyranges_1.32.0.tar.gz
Windows Binary (x86_64)	plyranges_1.32.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	plyranges_1.32.0.tgz
macOS Binary (sonoma-arm64)	plyranges_1.32.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/plyranges
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/plyranges
Package Short Url	https://bioconductor.org/packages/plyranges/
Package Downloads Report	Download Stats