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