raer
This is the development version of raer; for the stable release version, see raer.
RNA editing tools in R
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Alignment, Annotation, Coverage, Epitranscriptomics, FeatureExtraction, MultipleComparison, RNASeq, Sequencing, SingleCell, Software |
| Version | 1.11.1 |
| In Bioconductor since | BioC 3.18 (R-4.3) (3 years) |
| License | MIT + file LICENSE |
| Depends | |
| Imports | stats, methods, GenomicRanges, IRanges, Rsamtools, BSgenome, Biostrings, SummarizedExperiment, SingleCellExperiment, S4Vectors, Seqinfo, 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_1.11.1.tar.gz |
| Windows Binary (x86_64) | raer_1.11.1.zip |
| macOS Binary (big-sur-x86_64) | raer_1.11.1.tgz |
| macOS Binary (sonoma-arm64) | raer_1.11.1.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 |