DOI: 10.18129/B9.bioc.RLSeq  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see RLSeq.

RLSeq: An analysis package for R-loop mapping data

Bioconductor version: 3.16

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")):


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


biocViews Classification, Coverage, Epigenetics, Sequencing, Software, Transcriptomics
Version 1.4.1
In Bioconductor since BioC 3.14 (R-4.1) (1.5 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
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
URL https://github.com/Bishop-Laboratory/RLSeq https://bishop-laboratory.github.io/RLSeq/
BugReports https://github.com/Bishop-Laboratory/RLSeq/issues
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Source Package RLSeq_1.4.1.tar.gz
Windows Binary RLSeq_1.4.1.zip
macOS Binary (x86_64) RLSeq_1.4.1.tgz
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