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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 (3.19)

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 freshairfamily.org>

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

Installation

To install this package, start R (version "4.4") 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")
CoSIA_Intro HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews BiologicalQuestion, DataImport, GUI, GeneExpression, MultipleComparison, Software, ThirdPartyClient
Version 1.3.0
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), 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
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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Build Report Build Report

Package Archives

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

Source Package CoSIA_1.3.0.tar.gz
Windows Binary CoSIA_1.3.0.zip
macOS Binary (x86_64) CoSIA_1.3.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/CoSIA
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CoSIA
Bioc Package Browser https://code.bioconductor.org/browse/CoSIA/
Package Short Url https://bioconductor.org/packages/CoSIA/
Package Downloads Report Download Stats