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RLSeq

RLSeq: An analysis package for R-loop mapping data

Bioconductor version: Release (3.17)

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

Details

biocViews Classification, Coverage, Epigenetics, Sequencing, Software, Transcriptomics
Version 1.6.0
In Bioconductor since BioC 3.14 (R-4.1) (2 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
Linking To
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
System Requirements
Enhances
URL https://github.com/Bishop-Laboratory/RLSeq https://bishop-laboratory.github.io/RLSeq/
Bug Reports https://github.com/Bishop-Laboratory/RLSeq/issues
See More
Depends On Me
Imports Me
Suggests Me
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Build Report  

Package Archives

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

Source Package RLSeq_1.6.0.tar.gz
Windows Binary RLSeq_1.6.0.zip
macOS Binary (x86_64) RLSeq_1.6.0.tgz
macOS Binary (arm64) RLSeq_1.5.2.tgz
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