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An Investigation Across Different Species and Tissues

Bioconductor version: Release (3.18)

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.

Author: Anisha Haldar [aut] , Vishal H. Oza [aut] , Amanda D. Clark [cre, aut] , Nathaniel S. DeVoss [aut] , Brittany N. Lasseigne [aut]

Maintainer: Amanda D. Clark <amanda at>

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


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

if (!require("BiocManager", quietly = TRUE))


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


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

CoSIA_Intro HTML R Script
Reference Manual PDF


biocViews BiologicalQuestion, DataImport, GUI, GeneExpression, MultipleComparison, Software, ThirdPartyClient
Version 1.2.0
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
License MIT + file LICENSE
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),>= 3.12.0),>= 3.12.0),>= 3.12.0),>= 3.12.0),>= 3.12.0),>= 3.12.0), AnnotationDbi(>= 1.52.0), biomaRt(>= 2.46.3), homologene (>=, annotationTools(>= 1.64.0), readr (>= 2.1.1), tidyselect (>= 1.1.2), stats (>= 4.1.2)
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Suggests BiocStyle(>= 2.22.0), tidyverse (>= 1.3.1), knitr (>= 1.42), rmarkdown (>= 2.20), testthat (>= 3.1.6), qpdf (>= 1.3.0)
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Follow Installation instructions to use this package in your R session.

Source Package CoSIA_1.2.0.tar.gz
Windows Binary
macOS Binary (x86_64) CoSIA_1.2.0.tgz
macOS Binary (arm64) CoSIA_1.2.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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