Package: RNAAgeCalc 1.17.0

Xu Ren

RNAAgeCalc: A multi-tissue transcriptional age calculator

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.

Authors:Xu Ren [aut, cre], Pei Fen Kuan [aut]

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RNAAgeCalc.pdf |RNAAgeCalc.html✨
RNAAgeCalc/json (API)
NEWS

# Install 'RNAAgeCalc' in R:

install.packages('RNAAgeCalc', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/reese3928/rnaagecalc/issues

Datasets:

fpkm - An example of FPKM data
rawcount - An example of RNASeq counts data

On BioConductor:RNAAgeCalc-1.17.0(bioc 3.20)RNAAgeCalc-1.16.0(bioc 3.19)

bioconductor-package

4 exports 0.36 score 157 dependencies 2 mentions

Last updated 2 months agofrom:450b97ec87

Exports:count2FPKM makeplot predict_age predict_age_fromse

Dependencies:abind AnnotationDbi askpass backports base64enc BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome bslib bumphunter cachem checkmate cli clipr cluster codetools colorspace cpp11 crayon curl data.table DBI DelayedArray derfinder derfinderHelper digest doRNG downloader dplyr evaluate fansi farver fastmap fontawesome foreach foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicFiles GenomicRanges GEOquery ggplot2 glue gridExtra gtable highr Hmisc hms htmlTable htmltools htmlwidgets httr impute IRanges isoband iterators jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme nnet openssl org.Hs.eg.db pillar pkgconfig plogr plyr png prettyunits progress purrr qvalue R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RCurl readr recount rentrez reshape2 restfulr Rhtslib rjson rlang rmarkdown rngtools rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors sass scales snow SparseArray statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex tzdb UCSC.utils utf8 VariantAnnotation vctrs viridis viridisLite vroom withr xfun XML xml2 XVector yaml zlibbioc

RNAAgeCalc: A multi-tissue transcriptional age calculator

Xu Ren and Pei Fen Kuan

Rendered fromRNAAge-vignette.Rmdusingknitr::rmarkdownon Jun 13 2024.

Last update: 2020-06-24
Started: 2020-02-13

Help page	Topics
Converting gene expression data from raw count to FPKM	count2FPKM
An example of FPKM data	fpkm
Make plot to visualize RNA age	makeplot
Calculate RNA age	predict_age
Calculate RNA age using SummarizedExperiment	predict_age_fromse
An example of RNASeq counts data	rawcount

Package: RNAAgeCalc 1.17.0

RNAAgeCalc: A multi-tissue transcriptional age calculator

RNAAgeCalc: A multi-tissue transcriptional age calculator

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)