RLSeq

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.19 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see RLSeq.

RLSeq: An analysis package for R-loop mapping data


Bioconductor version: Release (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")

BiocManager::install("RLSeq")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

Reference Manual PDF

Details

biocViews Classification, Coverage, Epigenetics, Sequencing, Software, Transcriptomics
Version 1.10.0
In Bioconductor since BioC 3.14 (R-4.1) (3 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
Windows Binary (x86_64) RLSeq_1.10.0.zip
macOS Binary (x86_64)
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
Package Short Url https://bioconductor.org/packages/RLSeq/
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