raer
RNA editing tools in R
Bioconductor version: Release (3.20)
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("raer")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Alignment, Annotation, Coverage, Epitranscriptomics, FeatureExtraction, MultipleComparison, RNASeq, Sequencing, SingleCell, Software |
| Version | 1.4.0 |
| 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 |
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.
| Source Package | raer_1.4.0.tar.gz |
| Windows Binary (x86_64) | raer_1.4.0.zip (64-bit only) |
| macOS Binary (x86_64) | raer_1.4.0.tgz |
| macOS Binary (arm64) | raer_1.3.1.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 |