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Bioconductor - CoSIA (development version)

CoSIA

This is the development version of CoSIA; for the stable release version, see CoSIA.

An Investigation Across Different Species and Tissues

Bioconductor version: Development (3.22)

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] ORCID: 0000-0002-1395-9793 , Vishal H. Oza [aut] ORCID: 0000-0001-6990-0267 , Amanda D. Clark [cre, aut] ORCID: 0000-0002-1186-3114 , Nathaniel S. DeVoss [aut] ORCID: 0000-0003-0465-2770 , Brittany N. Lasseigne [aut] ORCID: 0000-0002-1642-8904

Maintainer: Amanda D. Clark <amanda at freshairfamily.org>

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

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("CoSIA")

Details biocViews BiologicalQuestion, DataImport, GUI, GeneExpression, MultipleComparison, Software, ThirdPartyClient Version 1.9.0 In Bioconductor since BioC 3.17 (R-4.3) (2 years) 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), 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) System Requirements URL https://www.lasseigne.org/ Bug Reports https://github.com/lasseignelab/CoSIA/issues See More Package Archives

Follow Installation instructions to use this package in your R session.

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