RLSeq

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

RLSeq: An analysis package for R-loop mapping data

Bioconductor version: 3.18

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>

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

Installation

To install this package, start R (version "4.3") 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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Classification, Coverage, Epigenetics, Sequencing, Software, Transcriptomics
Version	1.5.2
In Bioconductor since	BioC 3.14 (R-4.1) (2.5 years)
License	MIT + file LICENSE
Depends	R (>= 4.2.0)
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
System Requirements
URL	https://github.com/Bishop-Laboratory/RLSeq https://bishop-laboratory.github.io/RLSeq/
Bug Reports	https://github.com/Bishop-Laboratory/RLSeq/issues

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
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	RLSeq_1.5.2.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/RLSeq
Source Repository (Developer Access)	git clone [email protected]:packages/RLSeq
Bioc Package Browser	https://code.bioconductor.org/browse/RLSeq/
Package Short Url	https://bioconductor.org/packages/RLSeq/
Package Downloads Report	Download Stats