raer

This is the development version of raer; for the stable release version, see raer.

RNA editing tools in R

Bioconductor version: Development (3.21)

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] (ORCID: ), Kristen Wells-Wrasman [aut] (ORCID: ), Ryan Sheridan [ctb] (ORCID: ), Jay Hesselberth [ctb] (ORCID: ), RNA Bioscience Initiative [cph, fnd]

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

Citation (from within R, enter citation("raer")):

Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

Introduction	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Alignment, Annotation, Coverage, Epitranscriptomics, FeatureExtraction, MultipleComparison, RNASeq, Sequencing, SingleCell, Software
Version	1.5.0
In Bioconductor since	BioC 3.18 (R-4.3) (1 year)
License	MIT + file LICENSE
Depends
Imports	stats, methods, GenomicRanges, IRanges, Rsamtools, BSgenome, Biostrings, SummarizedExperiment, SingleCellExperiment, S4Vectors, GenomeInfoDb, GenomicAlignments, GenomicFeatures, BiocGenerics, BiocParallel, rtracklayer, Matrix, cli
System Requirements	GNU make
URL	https://rnabioco.github.io/raer https://github.com/rnabioco/raer
Bug Reports	https://github.com/rnabioco/raer/issues

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, txdbmaker
Linking To	Rhtslib
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	raer_1.5.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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