Package: CoSIA
Type: Package
Title: An Investigation Across Different Species and Tissues
Version: 1.12.1
Authors@R: 
  c(person(given = "Anisha",
           family = "Haldar",
           role = "aut",
           comment = c(ORCID = "0000-0002-1395-9793")),
    person(given = c("Vishal", "H."),
           family = "Oza",
           role = "aut",
           comment = c(ORCID = "0000-0001-6990-0267")),
    person(given = c("Amanda", "D."),
           family = "Clark",
           role = c("aut"),
           email = "clarkaduab@gmail.com",
           comment = c(ORCID = "0000-0002-1186-3114")),
    person(given = c("Anthony", "B."),
           family = "Crumley",
           role = c("cre", "aut"),
           email = "acrumley@uab.edu",
           comment = c(ORCID = "0009-0004-7347-4722")),
    person(given = c("Nathaniel", "S."),
           family = "DeVoss",
           role = "aut",
           comment = c(ORCID = "0000-0003-0465-2770")),
    person(given = c("Brittany", "N."),
           family = "Lasseigne",
           role = c("aut"),
           comment = c(ORCID = "0000-0002-1642-8904")))
Description: Cross-Species Investigation and Analysis (CoSIA) is a
        package that provides researchers with an alternative
        methodology for comparing across species and tissues using
        normal wild-type RNA-Seq Gene Expression data from Bgee. Using
        RNA-Seq Gene Expression data, CoSIA provides multiple
        visualization tools to explore the transcriptome diversity and
        variation across genes, tissues, and species. CoSIA uses the
        Coefficient of Variation and Shannon Entropy and Specificity to
        calculate transcriptome diversity and variation. CoSIA also
        provides additional conversion tools and utilities to provide a
        streamlined methodology for cross-species comparison.
License: MIT + file LICENSE
Encoding: UTF-8
Depends: R (>= 4.3.0), methods (>= 4.3.0), ExperimentHub (>= 2.7.0)
Imports: dplyr (>= 1.0.7), magrittr (>= 2.0.1), RColorBrewer (>=
        1.1-2), tidyr (>= 1.2.0), plotly (>= 4.10.0), stringr (>=
        1.4.0), ggplot2 (>= 3.3.5), tibble (>= 3.1.7), org.Hs.eg.db (>=
        3.12.0), org.Mm.eg.db (>= 3.12.0), org.Dr.eg.db (>= 3.12.0),
        org.Ce.eg.db (>= 3.12.0), org.Dm.eg.db (>= 3.12.0),
        org.Rn.eg.db (>= 3.12.0), AnnotationDbi (>= 1.52.0), biomaRt
        (>= 2.46.3), homologene (>= 1.4.68.19), annotationTools (>=
        1.64.0), readr (>= 2.1.1), tidyselect (>= 1.1.2), stats (>=
        4.1.2)
RoxygenNote: 7.3.3
Suggests: BiocStyle (>= 2.22.0), tidyverse (>= 1.3.1), knitr (>= 1.42),
        rmarkdown (>= 2.20), testthat (>= 3.1.6), qpdf (>= 1.3.0)
biocViews: Software, BiologicalQuestion, GeneExpression,
        MultipleComparison, ThirdPartyClient, DataImport, GUI
BugReports: https://github.com/lasseignelab/CoSIA/issues
URL: https://www.lasseigne.org/
VignetteBuilder: knitr
Config/testthat/edition: 3
Config/pak/sysreqs: cmake make libicu-dev libpng-dev libuv1-dev
        libxml2-dev libssl-dev libx11-dev zlib1g-dev
Repository: Bioconductor 3.23
Date/Publication: 2026-07-02 19:45:44 UTC
RemoteUrl: https://github.com/bioc/CoSIA
RemoteRef: RELEASE_3_23
RemoteSha: 67d68f3587f1cecc44cb5e6083f28ee608ef6168
NeedsCompilation: no
Packaged: 2026-07-02 21:08:23 UTC; root
Author: Anisha Haldar [aut] (ORCID: <https://orcid.org/0000-0002-1395-9793>),
  Vishal H. Oza [aut] (ORCID: <https://orcid.org/0000-0001-6990-0267>),
  Amanda D. Clark [aut] (ORCID: <https://orcid.org/0000-0002-1186-3114>),
  Anthony B. Crumley [cre, aut] (ORCID:
    <https://orcid.org/0009-0004-7347-4722>),
  Nathaniel S. DeVoss [aut] (ORCID:
    <https://orcid.org/0000-0003-0465-2770>),
  Brittany N. Lasseigne [aut] (ORCID:
    <https://orcid.org/0000-0002-1642-8904>)
Maintainer: Anthony B. Crumley <acrumley@uab.edu>