TEKRABber

This is the development version of TEKRABber; for the stable release version, see TEKRABber.

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

Bioconductor version: Development (3.18)

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>

Citation (from within R, enter citation("TEKRABber")):

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("TEKRABber")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("TEKRABber")

TEKRABber	HTML	R Script
Reference Manual	PDF
NEWS	Text

Details

biocViews	DifferentialExpression, GeneExpression, Normalization, Software, Transcription
Version	1.5.0
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
Linking To	Rcpp
Suggests	BiocStyle, ggpubr, rmarkdown, shiny, knitr, testthat (>= 3.0.0)
System Requirements
Enhances
URL	https://github.com/ferygood/TEKRABber
Bug Reports	https://github.com/ferygood/TEKRABber/issues

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	TEKRABber_1.5.0.tar.gz
Windows Binary	TEKRABber_1.5.0.zip
macOS Binary (x86_64)	TEKRABber_1.5.0.tgz
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/TEKRABber
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/
Package Downloads Report	Download Stats