TEKRABber is made to provide an 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 ortholog/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.
TEKRABber analysis pipeline includes 5 main functions:
1. orthologScale(): obtain orthology information and calculate scaling factor. 2. DECorrInputs(): create the input files for running DE/correlation analysis. 3. DEgeneTE(): run DE analysis on orthologs and transposable elements. 4. corrOrthologTE(): estimate correlation between selected orthologs and transposable elements. 5. appTEKRABber(): (optional) find first insight from data using an local webapp. Find more details in vignette or on the helping page, i.e. ?orthologScale
Yao-Chung Chen, Katja Nowick.
Maintainer: Yao-Chung Chen email@example.com
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