Package: TEKRABber 1.17.0

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_1.17.0.tar.gz
TEKRABber_1.17.0.zip(r-4.7)TEKRABber_1.17.0.zip(r-4.6)TEKRABber_1.17.0.zip(r-4.5)
TEKRABber_1.17.0.tgz(r-4.6-x86_64)TEKRABber_1.17.0.tgz(r-4.6-arm64)TEKRABber_1.17.0.tgz(r-4.5-x86_64)TEKRABber_1.17.0.tgz(r-4.5-arm64)
TEKRABber_1.17.0.tar.gz(r-4.7-arm64)TEKRABber_1.17.0.tar.gz(r-4.7-x86_64)TEKRABber_1.17.0.tar.gz(r-4.6-arm64)TEKRABber_1.17.0.tar.gz(r-4.6-x86_64)
TEKRABber_1.17.0.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.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

5.56 score 3 stars 20 scripts 361 downloads 6 exports 118 dependencies

Last updated from:147c15f0de. Checks:1 WARNING, 11 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING245
linux-devel-arm64NOTE570
linux-devel-x86_64NOTE612
source / vignettesOK378
linux-release-arm64NOTE590
linux-release-x86_64NOTE587
macos-release-arm64NOTE408
macos-release-x86_64NOTE707
macos-oldrel-arm64NOTE433
macos-oldrel-x86_64NOTE825
windows-develNOTE696
windows-releaseNOTE708
windows-oldrelNOTE746
wasm-releaseOK193

Exports:appTEKRABbercorrOrthologTEDECorrInputsDEgeneTEorthologScaleprepareRMSK

Dependencies:abindAnnotationDbiAnnotationHubapeglmaskpassbbmlebdsmatrixBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionbiomaRtBiostringsbitbit64bitopsblobcachemcigarilloclicodacodetoolscpp11crayoncurlDBIdbplyrDelayedArrayDESeq2doParalleldplyremdbookfarverfastmapfilelockforeachformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesggplot2gluegtablehmshttrhttr2IRangesisobanditeratorsjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimemvtnormnumDerivopensslpillarpkgconfigplyrpngprettyunitsprogresspurrrR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRcppNumericalRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7scalesSCBNSeqinfosnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectutf8vctrsviridisLitewithrXMLxml2XVectoryaml

TEKRABber

Yao-Chung Chen, Katja Nowick

Rendered fromTEKRABber.Rmdusingknitr::rmarkdownon May 26 2026.

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