DOI: 10.18129/B9.bioc.TEKRABber  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see TEKRABber.

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

Bioconductor version: 3.17

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.

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

Maintainer: Yao-Chung Chen <yao-chung.chen at fu-berlin.de>

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biocViews DifferentialExpression, GeneExpression, Normalization, Software, Transcription
Version 1.4.0
In Bioconductor since BioC 3.15 (R-4.2) (1.5 years)
License GPL (>= 2)
Depends R (>= 4.1)
Imports apeglm, biomaRt, dplyr, DESeq2, magrittr, Rcpp (>= 1.0.7), SCBN, SummarizedExperiment, stats, utils
LinkingTo Rcpp
Suggests BiocStyle, ggpubr, rmarkdown, shiny, knitr, testthat (>= 3.0.0)
URL https://github.com/ferygood/TEKRABber
BugReports https://github.com/ferygood/TEKRABber/issues
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Source Package TEKRABber_1.4.0.tar.gz
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macOS Binary (x86_64) TEKRABber_1.4.0.tgz
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Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/TEKRABber
Bioc Package Browser https://code.bioconductor.org/browse/TEKRABber/
Package Short Url https://bioconductor.org/packages/TEKRABber/
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