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raer
This is thedevelopment version of raer; for the stable release version, seeraer.
RNA editing tools in R
Bioconductor version: Development (3.23)
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("raer")):Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")# The following initializes usage of Bioc develBiocManager::install(version='devel')BiocManager::install("raer")For older versions of R, please refer to the appropriateBioconductor 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 | 1.9.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (2 years) |
| License | MIT + fileLICENSE |
| 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/raerhttps://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
FollowInstallation instructions to use this package in your R session.
| Source Package | raer_1.9.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | raer_1.9.0.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 |