rnaEditr
This is the development version of rnaEditr; for the stable release version, see rnaEditr.
Statistical analysis of RNA editing sites and hyper-editing regions
Bioconductor version: Development (3.24)
RNAeditr analyzes site-specific RNA editing events, as well as hyper-editing regions. The editing frequencies can be tested against binary, continuous or survival outcomes. Multiple covariate variables as well as interaction effects can also be incorporated in the statistical models.
Author: Lanyu Zhang [aut, cre], Gabriel Odom [aut], Tiago Silva [aut], Lissette Gomez [aut], Lily Wang [aut]
Maintainer: Lanyu Zhang <jennyzly2016 at gmail.com>
citation("rnaEditr")):
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("rnaEditr")
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("rnaEditr")| Introduction to rnaEditr | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DimensionReduction, Epigenetics, FeatureExtraction, GeneTarget, RNASeq, Regression, Software, Survival |
| Version | 1.23.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 years) |
| License | GPL-3 |
| Depends | R (>= 4.0) |
| Imports | GenomicRanges, IRanges, BiocGenerics, Seqinfo, bumphunter, S4Vectors, stats, survival, logistf, plyr, corrplot |
| System Requirements | |
| URL | https://github.com/TransBioInfoLab/rnaEditr |
| Bug Reports | https://github.com/TransBioInfoLab/rnaEditr/issues |
See More
| Suggests | knitr, rmarkdown, testthat |
| Linking To | |
| 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 | rnaEditr_1.23.0.tar.gz |
| Windows Binary (x86_64) | rnaEditr_1.23.0.zip |
| macOS Binary (big-sur-x86_64) | rnaEditr_1.23.0.tgz |
| macOS Binary (sonoma-arm64) | rnaEditr_1.23.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/rnaEditr |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/rnaEditr |
| Bioc Package Browser | https://code.bioconductor.org/browse/rnaEditr/ |
| Package Short Url | https://bioconductor.org/packages/rnaEditr/ |
| Package Downloads Report | Download Stats |