Package: TEKRABber
Type: Package
Title: An R package estimates the correlations of orthologs and
        transposable elements between two species
Version: 1.15.0
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, Seqinfo,
        magrittr, Rcpp (>= 1.0.7), rtracklayer, SCBN, stats, utils
LinkingTo: Rcpp
Depends: R (>= 4.3)
LazyData: false
Suggests: BiocStyle, GenomeInfoDb, bslib, ggplot2, ggpubr, plotly,
        rmarkdown, shiny, knitr, testthat (>= 3.0.0)
VignetteBuilder: knitr
VignetteEngine: knitr
RoxygenNote: 7.3.1
biocViews: DifferentialExpression, Normalization, Transcription,
        GeneExpression
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:14:57 UTC
RemoteUrl: https://github.com/bioc/TEKRABber
RemoteRef: HEAD
RemoteSha: ffc9f331f8ae86c2c474043813dae26e0dacb165
NeedsCompilation: yes
Packaged: 2025-10-30 13:41:30 UTC; root
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 4.6.0; x86_64-w64-mingw32; 2025-10-30 13:43:57 UTC; windows
Archs: x64
