TEKRABber-package: An R package estimates the correlations of orthologs and...
In ferygood/TEKRABber: An R package estimates the correlations of orthologs and transposable elements between two species
TEKRABber R Documentation
An R package estimates the correlations of orthologs and transposable
elements between two species
Description
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.
Details
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
Author(s)
Yao-Chung Chen, Katja Nowick.
Maintainer: Yao-Chung Chen yao-chung.chen@fu-berlin.de
ferygood/TEKRABber documentation built on Jan. 29, 2024, 6:34 p.m.
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| TEKRABber | R Documentation |
An R package estimates the correlations of orthologs and transposable elements between two species
Description
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.
Details
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
Author(s)
Yao-Chung Chen, Katja Nowick.
Maintainer: Yao-Chung Chen yao-chung.chen@fu-berlin.de
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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