Installation | Introduction | Description of RNASeq age calculator | Usage of RNASeq age calculator | Options in predict_age function | exprdata | tissue | exprtype | idtype | stype | signature | genelength | chronage | Example | Options in predict_age_fromse function | Visualization | Session info | References
Package: RNAAgeCalc 1.25.0
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:
RNAAgeCalc_1.25.0.tar.gz
RNAAgeCalc_1.25.0.zip(r-4.7)RNAAgeCalc_1.25.0.zip(r-4.6)RNAAgeCalc_1.25.0.zip(r-4.5)
RNAAgeCalc_1.25.0.tgz(r-4.6-any)RNAAgeCalc_1.25.0.tgz(r-4.5-any)
RNAAgeCalc_1.25.0.tar.gz(r-4.7-any)RNAAgeCalc_1.25.0.tar.gz(r-4.6-any)
RNAAgeCalc_1.25.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
RNAAgeCalc/json (API)
| # 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
On BioConductor:RNAAgeCalc-1.25.0(bioc 3.24)RNAAgeCalc-1.24.0(bioc 3.23)
rnaseqgeneexpressionbiological-ageelastic-netgene-expressiongenotype-tissue-expressionpredictionregularized-regressionrna-seq
Last updated from:d39b87dacb. Checks:8 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
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| bioc-checks | NOTE | 242 | ||
| linux-devel-x86_64 | NOTE | 523 | ||
| source / vignettes | OK | 486 | ||
| linux-release-x86_64 | NOTE | 499 | ||
| macos-release-arm64 | NOTE | 308 | ||
| macos-oldrel-arm64 | NOTE | 428 | ||
| windows-devel | NOTE | 443 | ||
| windows-release | NOTE | 442 | ||
| windows-oldrel | NOTE | 388 | ||
| wasm-release | OK | 205 |
Exports:count2FPKMmakeplotpredict_agepredict_age_fromse
Dependencies:abindAnnotationDbiaskpassbackportsbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomebslibbumphuntercachemcheckmatecigarilloclicliprclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArrayderfinderderfinderHelperdigestdoRNGdownloaderdplyrevaluatefarverfastmapfilelockfontawesomeforeachforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicFilesGenomicRangesGEOqueryggplot2gluegridExtragtablehighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2imputeIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMatrixMatrixGenericsmatrixStatsmemoisemimennetopensslorg.Hs.eg.dbpillarpkgconfigplyrpngprettyunitsprogresspurrrqvalueR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRCurlreadrrecountrentrezreshape2restfulrRhtslibrjsonrlangrmarkdownrngtoolsrpartRsamtoolsRSQLiterstudioapirtracklayerrvestS4ArraysS4VectorsS7sassscalesselectrSeqinfosnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytextzdbUCSC.utilsutf8VariantAnnotationvctrsviridisLitevroomwithrxfunXMLxml2XVectoryaml
Readme and manuals
Help Manual
| 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 |
