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raer

RNA editing tools in R

Bioconductor version: 3.23 · Package version: 1.10.0

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.

Installation

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

BiocManager::install("raer")

Details

MaintainerKent Riemondy <kent.riemondy@gmail.com>
AuthorKent Riemondy [aut, cre] (ORCID: <https://orcid.org/0000-0003-0750-1273>), Kristen Wells-Wrasman [aut] (ORCID: <https://orcid.org/0000-0002-7466-8164>), Ryan Sheridan [ctb] (ORCID: <https://orcid.org/0000-0003-4012-3147>), Jay Hesselberth [ctb] (ORCID: <https://orcid.org/0000-0002-6299-179X>), RNA Bioscience Initiative [cph, fnd]
LicenseMIT + file LICENSE
URLhttps://rnabioco.github.io/raer, https://github.com/rnabioco/raer
Bug Reportshttps://github.com/rnabioco/raer/issues
System RequirementsGNU make
Downloads rank257
Source branchRELEASE_3_23
biocViewsAlignment, Annotation, Coverage, Epitranscriptomics, FeatureExtraction, MultipleComparison, RNASeq, Sequencing, SingleCell, Software

Documentation

Download

Dependencies

Imports: stats, methods, GenomicRanges, IRanges, Rsamtools, BSgenome, Biostrings, SummarizedExperiment, SingleCellExperiment, S4Vectors, Seqinfo, GenomeInfoDb, GenomicAlignments, GenomicFeatures, BiocGenerics, BiocParallel, rtracklayer, Matrix, 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, txdbmaker