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 (3.21)
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] (ORCID:
Maintainer: Yao-Chung Chen <yao-chung.chen at fu-berlin.de>
citation("TEKRABber")):
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, Normalization, Software, Transcription |
| Version | 1.11.0 |
| In Bioconductor since | BioC 3.15 (R-4.2) (2.5 years) |
| License | LGPL (>=3) |
| Depends | R (>= 4.3) |
| Imports | apeglm, biomaRt, dplyr, doParallel, DESeq2, foreach, GenomeInfoDb, magrittr, Rcpp (>= 1.0.7), rtracklayer, SCBN, stats, utils |
| System Requirements | |
| URL | https://github.com/ferygood/TEKRABber |
| Bug Reports | https://github.com/ferygood/TEKRABber/issues |
See More
| Suggests | BiocStyle, bslib, ggplot2, ggpubr, plotly, rmarkdown, shiny, knitr, testthat (>= 3.0.0) |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | TEKRABber_1.11.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| 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 |