RNAAgeCalc
This is the development version of RNAAgeCalc; for the stable release version, see RNAAgeCalc.
A multi-tissue transcriptional age calculator
Bioconductor version: Development (3.24)
It has been shown that both DNA methylation and RNA transcription are linked to chronological age and age related diseases. Several estimators have been developed to predict human aging from DNA level and RNA level. Most of the human transcriptional age predictor are based on microarray data and limited to only a few tissues. To date, transcriptional studies on aging using RNASeq data from different human tissues is limited. The aim of this package is to provide a tool for across-tissue and tissue-specific transcriptional age calculation based on GTEx RNASeq data.
Author: Xu Ren [aut, cre], Pei Fen Kuan [aut]
Maintainer: Xu Ren <xuren2120 at gmail.com>
citation("RNAAgeCalc")):
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("RNAAgeCalc")
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("RNAAgeCalc")| RNAAgeCalc | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, RNASeq, Software |
| Version | 1.25.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (6.5 years) |
| License | GPL-2 |
| Depends | R (>= 3.6) |
| Imports | ggplot2, recount, impute, AnnotationDbi, org.Hs.eg.db, stats, SummarizedExperiment, methods |
| System Requirements | |
| URL | https://github.com/reese3928/RNAAgeCalc |
| Bug Reports | https://github.com/reese3928/RNAAgeCalc/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 | RNAAgeCalc_1.25.0.tar.gz |
| Windows Binary (x86_64) | RNAAgeCalc_1.25.0.zip |
| macOS Binary (big-sur-x86_64) | RNAAgeCalc_1.25.0.tgz |
| macOS Binary (sonoma-arm64) | RNAAgeCalc_1.25.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/RNAAgeCalc |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/RNAAgeCalc |
| Bioc Package Browser | https://code.bioconductor.org/browse/RNAAgeCalc/ |
| Package Short Url | https://bioconductor.org/packages/RNAAgeCalc/ |
| Package Downloads Report | Download Stats |