raer

DOI: 10.18129/B9.bioc.raer  

RNA editing tools in R

Bioconductor version: Release (3.18)

Toolkit for identification and statistical testing of RNA editing signals from within R. Provides support for identifying sites from bulk-RNA and single cell RNA-seq datasets, and general methods for extraction of allelic read counts from alignment files. Facilitates annotation and exploratory analysis of editing signals using Bioconductor packages and resources.

Author: Kent Riemondy [aut, cre] , Kristen Wells-Wrasman [aut] , Ryan Sheridan [ctb] , Jay Hesselberth [ctb] , RNA Bioscience Initiative [cph, fnd]

Maintainer: Kent Riemondy <kent.riemondy at gmail.com>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("raer")

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("raer")

 

HTML	R Script	Introduction
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Alignment, Annotation, Coverage, Epitranscriptomics, FeatureExtraction, MultipleComparison, RNASeq, Sequencing, SingleCell, Software
Version	1.0.0
In Bioconductor since	BioC 3.18 (R-4.3) (< 6 months)
License	MIT + file LICENSE
Depends
Imports	stats, methods, data.table, GenomicRanges, IRanges, Rsamtools, BSgenome, Biostrings, SummarizedExperiment, SingleCellExperiment, S4Vectors, GenomeInfoDb, GenomicAlignments, GenomicFeatures, BiocGenerics, BiocParallel, rtracklayer, Matrix, R.utils, cli
LinkingTo	Rhtslib
Suggests	testthat (>= 3.0.0), knitr, DESeq2, edgeR, limma, rmarkdown, BiocStyle, ComplexHeatmap, TxDb.Hsapiens.UCSC.hg38.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh38, BSgenome.Hsapiens.NCBI.GRCh38, scater, scran, scuttle, AnnotationHub, covr, raerdata
SystemRequirements	GNU make
Enhances
URL	https://rnabioco.github.io/raer https://github.com/rnabioco/raer
BugReports	https://github.com/rnabioco/raer/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	raer_1.0.0.tar.gz
Windows Binary	raer_1.0.0.zip
macOS Binary (x86_64)	raer_1.0.0.tgz
macOS Binary (arm64)	raer_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/raer
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/raer
Bioc Package Browser	https://code.bioconductor.org/browse/raer/
Package Short Url	https://bioconductor.org/packages/raer/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.18	Source Archive