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Bioconductor - raer (development version)

raer

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

RNA editing tools in R

Bioconductor version: Development (3.22)

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: 0000-0003-0750-1273 , Kristen Wells-Wrasman [aut] ORCID: 0000-0002-7466-8164 , Ryan Sheridan [ctb] ORCID: 0000-0003-4012-3147 , Jay Hesselberth [ctb] ORCID: 0000-0002-6299-179X , 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")

Details biocViews Alignment, Annotation, Coverage, Epitranscriptomics, FeatureExtraction, MultipleComparison, RNASeq, Sequencing, SingleCell, Software Version 1.7.0 In Bioconductor since BioC 3.18 (R-4.3) (1.5 years) 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 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, 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.

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