RLSeq

DOI: 10.18129/B9.bioc.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 (3.15)

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 "4.2") and enter:

if (!requireNamespace("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")

 

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 1.1.0
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_1.1.0.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
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

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