Package: TEKRABber 1.16.0

Yao-Chung Chen

TEKRABber: An R package estimates the correlations of orthologs and transposable elements between two species

TEKRABber is made to provide a user-friendly pipeline for comparing orthologs and transposable elements (TEs) between two species. It considers the orthology confidence between two species from BioMart to normalize expression counts and detect differentially expressed orthologs/TEs. Then it provides one to one correlation analysis for desired orthologs and TEs. There is also an app function to have a first insight on the result. Users can prepare orthologs/TEs RNA-seq expression data by their own preference to run TEKRABber following the data structure mentioned in the vignettes.

Authors:Yao-Chung Chen [aut, cre], Katja Nowick [aut]

TEKRABber_1.16.0.tar.gz
TEKRABber_1.16.0.zip(r-4.7)TEKRABber_1.16.0.zip(r-4.6)TEKRABber_1.16.0.zip(r-4.5)
TEKRABber_1.16.0.tgz(r-4.6-x86_64)TEKRABber_1.16.0.tgz(r-4.6-arm64)TEKRABber_1.16.0.tgz(r-4.5-x86_64)TEKRABber_1.16.0.tgz(r-4.5-arm64)
TEKRABber_1.16.0.tar.gz(r-4.7-arm64)TEKRABber_1.16.0.tar.gz(r-4.7-x86_64)TEKRABber_1.16.0.tar.gz(r-4.6-arm64)TEKRABber_1.16.0.tar.gz(r-4.6-x86_64)
TEKRABber_1.16.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
TEKRABber/json (API)

# Install 'TEKRABber' in R:
install.packages('TEKRABber', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ferygood/tekrabber/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • ctInputDE - Input expression data of gene/TE for differentially expressed analysis within same species
  • fetchDataHmChimp - Example output comparing human and chimpanzee data using orhtologScale
  • hg38_panTro6_rmsk - Repeatmasker track annotations with human and chimpanzee
  • speciesCounts - Gene/TE expression data from human/chimpanzee brain RNA-seq

On BioConductor:TEKRABber-1.17.0(bioc 3.24)TEKRABber-1.16.0(bioc 3.23)

differentialexpressionnormalizationtranscriptiongeneexpressionbioconductorcpp

5.62 score 3 stars 23 scripts 340 downloads 6 exports 118 dependencies

Last updated from:59f88f1a88 (on RELEASE_3_23). Checks:1 WARNING, 11 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksWARNING218
linux-devel-arm64NOTE595
linux-devel-x86_64NOTE541
source / vignettesOK355
linux-release-arm64NOTE572
linux-release-x86_64NOTE589
macos-release-arm64NOTE385
macos-release-x86_64NOTE1091
macos-oldrel-arm64NOTE431
macos-oldrel-x86_64NOTE1050
windows-develNOTE738
windows-releaseNOTE766
windows-oldrelNOTE698
wasm-releaseOK178

Exports:appTEKRABbercorrOrthologTEDECorrInputsDEgeneTEorthologScaleprepareRMSK

Dependencies:abindAnnotationDbiAnnotationHubapeglmaskpassbbmlebdsmatrixBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionbiomaRtBiostringsbitbit64bitopsblobcachemcigarilloclicodacodetoolscpp11crayoncurlDBIdbplyrDelayedArrayDESeq2doParalleldplyremdbookfarverfastmapfilelockforeachformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesggplot2gluegtablehmshttrhttr2IRangesisobanditeratorsjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimemvtnormnumDerivopensslpillarpkgconfigplyrpngprettyunitsprogresspurrrR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRcppNumericalRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7scalesSCBNSeqinfosnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectutf8vctrsviridisLitewithrXMLxml2XVectoryaml

TEKRABber

Yao-Chung Chen, Katja Nowick

Rendered fromTEKRABber.Rmdusingknitr::rmarkdownon Jun 02 2026.

Last update: 2024-02-23
Started: 2021-11-29