plyranges

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see plyranges.

A fluent interface for manipulating GenomicRanges

Bioconductor version: 3.19

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] , Michael Lawrence [aut, ctb], Dianne Cook [aut, ctb], Spencer Nystrom [ctb] , Pierre-Paul Axisa [ctb], Michael Love [ctb, cre]

Maintainer: Michael Love <michaelisaiahlove at gmail.com>

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

Installation

To install this package, start R (version "4.4") 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

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Coverage, DataRepresentation, Infrastructure, Software, WorkflowStep

Version 1.24.0

In Bioconductor since BioC 3.7 (R-3.5) (6.5 years)

License Artistic-2.0

Depends R (>= 3.5), BiocGenerics, IRanges(>= 2.12.0), GenomicRanges(>= 1.28.4)

Imports methods, dplyr, rlang (>= 0.2.0), magrittr, tidyselect (>= 1.0.0), rtracklayer, GenomicAlignments, GenomeInfoDb, Rsamtools, S4Vectors(>= 0.23.10), utils

System Requirements

URL

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

Imports Me BOBaFIT, BUSpaRse, Damsel, GenomicPlot, InPAS, SARC, cfDNAPro, katdetectr, mariner, methylCC, multicrispr, nearBynding, nullranges, plotgardener, plyinteractions, tidyomics, fluentGenomics, MOCHA

Suggests Me extraChIPs, memes, svaNUMT, svaRetro, tidyCoverage, CTCF

Links To Me

Build Report Build Report

Package Archives

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

Source Package plyranges_1.24.0.tar.gz

Windows Binary (x86_64) plyranges_1.24.0.zip (64-bit only)

macOS Binary (x86_64) plyranges_1.24.0.tgz

macOS Binary (arm64)

Source Repository git clone https://git.bioconductor.org/packages/plyranges

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/plyranges

Bioc Package Browser https://code.bioconductor.org/browse/plyranges/

Package Short Url https://bioconductor.org/packages/plyranges/

Package Downloads Report Download Stats