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: 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("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 |
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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
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/ |
| Package Downloads Report | Download Stats |