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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>

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

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")
Introduction HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Alignment, Annotation, Coverage, Epitranscriptomics, FeatureExtraction, MultipleComparison, RNASeq, Sequencing, SingleCell, Software
Version 1.0.2
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
System Requirements GNU make
URL https://rnabioco.github.io/raer https://github.com/rnabioco/raer
Bug Reports https://github.com/rnabioco/raer/issues
See More
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
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_1.0.2.tar.gz
Windows Binary raer_1.0.2.zip
macOS Binary (x86_64) raer_1.0.2.tgz
macOS Binary (arm64) raer_1.0.2.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