RLSeq

DOI: 10.18129/B9.bioc.RLSeq    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see RLSeq.

RLSeq: An analysis package for R-loop mapping data

Bioconductor version: 3.14

RLSeq is a toolkit for analyzing and evaluating R-loop mapping datasets. RLSeq serves two primary purposes: (1) to facilitate the evaluation of dataset quality, and (2) to enable R-loop analysis in the context of publicly-available data sets from RLBase. The package is intended to provide a simple pipeline, called with the `RLSeq()` function, which performs all main analyses. Individual functions are also accessible and provide custom analysis capabilities. Finally an HTML report is generated with `report()`.

Author: Henry Miller [aut, cre, cph] , Daniel Montemayor [ctb] , Simon Levy [ctb] , Anna Vines [ctb] , Alexander Bishop [ths, cph]

Maintainer: Henry Miller <millerh1 at uthscsa.edu>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("RLSeq")

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("RLSeq")

 

HTML	R Script	Analyzing R-loop Data with RLSeq
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Classification, Coverage, Epigenetics, Sequencing, Software, Transcriptomics
Version	1.0.0
In Bioconductor since	BioC 3.14 (R-4.1) (< 6 months)
License	MIT + file LICENSE
Depends	R (>= 4.1.0)
Imports	dplyr, ggplot2, RColorBrewer, grid, regioneR, valr, caretEnsemble, GenomicFeatures, rtracklayer, GenomicRanges, GenomeInfoDb, ComplexHeatmap, AnnotationHub, VennDiagram, callr, circlize, ggplotify, ggprism, methods, stats, RLHub, aws.s3, pheatmap
LinkingTo
Suggests	AnnotationDbi, BiocStyle, covr, lintr, rcmdcheck, DT, httr, jsonlite, kableExtra, kernlab, knitr, magick, MASS, org.Hs.eg.db, R.utils, randomForest, readr, rmarkdown, rpart, testthat (>= 3.0.0), tibble, tidyr, TxDb.Hsapiens.UCSC.hg19.knownGene, futile.logger
SystemRequirements
Enhances
URL	https://github.com/Bishop-Laboratory/RLSeq https://bishop-laboratory.github.io/RLSeq/
BugReports	https://github.com/Bishop-Laboratory/RLSeq/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	RLSeq_1.0.0.tar.gz
Windows Binary	RLSeq_1.0.0.zip
macOS 10.13 (High Sierra)	RLSeq_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/RLSeq
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/RLSeq
Package Short Url	https://bioconductor.org/packages/RLSeq/
Package Downloads Report	Download Stats