Package: TEKRABber
Type: Package
Title: An R package estimates the correlations of orthologs and
        transposable elements between two species
Version: 1.12.0
Description: 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.   
Authors@R: c(person("Yao-Chung", "Chen", email = "yao-chung.chen@fu-berlin.de", 
    role = c("aut", "cre"), comment = c(ORCID = "0000-0002-9927-9130")),
    person("Katja", "Nowick", email = "katja.nowick@fu-berlin.de", 
    role = c("aut"), comment = c(ORCID = "0000-0003-3993-4479")))
URL: https://github.com/ferygood/TEKRABber
BugReports: https://github.com/ferygood/TEKRABber/issues
Encoding: UTF-8
License: LGPL (>=3)
Imports: apeglm, biomaRt, dplyr, doParallel, DESeq2, foreach,
        GenomeInfoDb, magrittr, Rcpp (>= 1.0.7), rtracklayer, SCBN,
        stats, utils
LinkingTo: Rcpp
Depends: R (>= 4.3)
LazyData: false
Suggests: BiocStyle, bslib, ggplot2, ggpubr, plotly, rmarkdown, shiny,
        knitr, testthat (>= 3.0.0)
VignetteBuilder: knitr
VignetteEngine: knitr
RoxygenNote: 7.3.1
biocViews: DifferentialExpression, Normalization, Transcription,
        GeneExpression
git_url: https://git.bioconductor.org/packages/TEKRABber
git_branch: RELEASE_3_21
git_last_commit: 9d1b124
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
NeedsCompilation: yes
Packaged: 2025-04-16 04:10:31 UTC; biocbuild
Author: Yao-Chung Chen [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-9927-9130>),
  Katja Nowick [aut] (ORCID: <https://orcid.org/0000-0003-3993-4479>)
Maintainer: Yao-Chung Chen <yao-chung.chen@fu-berlin.de>
Built: R 4.5.0; x86_64-w64-mingw32; 2025-04-16 15:41:53 UTC; windows
Archs: x64
