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RLSeq

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

RLSeq: An analysis package for R-loop mapping data


Bioconductor version: Development (3.19)

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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Classification, Coverage, Epigenetics, Sequencing, Software, Transcriptomics
Version 1.9.0
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
See More
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
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Package Archives

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

Source Package RLSeq_1.9.0.tar.gz
Windows Binary RLSeq_1.9.0.zip
macOS Binary (x86_64) RLSeq_1.9.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/RLSeq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/RLSeq
Bioc Package Browser https://code.bioconductor.org/browse/RLSeq/
Package Short Url https://bioconductor.org/packages/RLSeq/
Package Downloads Report Download Stats