Package: TEKRABber 1.11.0

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_1.11.0.tar.gz
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TEKRABber.pdf |TEKRABber.html✨
TEKRABber/json (API)

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

Peer review:

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-1.11.0(bioc 3.21)TEKRABber-1.10.0(bioc 3.20)

differentialexpressionnormalizationtranscriptiongeneexpressionbioconductor

5.37 score 3 stars 13 scripts 357 downloads 6 exports 122 dependencies

Last updated 23 days agofrom:3e1203ec0e. Checks:OK: 1 NOTE: 3 WARNING: 5. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-win-x86_64WARNINGOct 31 2024
R-4.5-linux-x86_64NOTEOct 31 2024
R-4.4-win-x86_64WARNINGOct 31 2024
R-4.4-mac-x86_64WARNINGOct 31 2024
R-4.4-mac-aarch64NOTEOct 31 2024
R-4.3-win-x86_64WARNINGOct 31 2024
R-4.3-mac-x86_64WARNINGOct 31 2024
R-4.3-mac-aarch64NOTEOct 31 2024

Exports:appTEKRABbercorrOrthologTEDECorrInputsDEgeneTEorthologScaleprepareRMSK

Dependencies:abindAnnotationDbiapeglmaskpassbbmlebdsmatrixBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobcachemclicodacodetoolscolorspacecpp11crayoncurlDBIdbplyrDelayedArrayDESeq2digestdoParalleldplyremdbookfansifarverfastmapfilelockforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegtablehmshttrhttr2IRangesisobanditeratorsjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellmvtnormnlmenumDerivopensslpillarpkgconfigplogrplyrpngprettyunitsprogresspurrrR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRcppNumericalRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalesSCBNsnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXMLxml2XVectoryamlzlibbioc

TEKRABber

Yao-Chung Chen, Katja Nowick

Rendered fromTEKRABber.Rmdusingknitr::rmarkdownon Oct 31 2024.

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