CoSIA

DOI: 10.18129/B9.bioc.CoSIA  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see CoSIA.

An Investigation Across Different Species and Tissues

Bioconductor version: 3.17

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>

Installation

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

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

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")

 

HTML	R Script	CoSIA_Intro
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	BiologicalQuestion, DataImport, GUI, GeneExpression, MultipleComparison, Software, ThirdPartyClient
Version	1.0.0
In Bioconductor since	BioC 3.17 (R-4.3) (< 6 months)
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)
LinkingTo
Suggests	BiocStyle(>= 2.22.0), tidyverse (>= 1.3.1), knitr (>= 1.42), rmarkdown (>= 2.20), testthat (>= 3.1.6), qpdf (>= 1.3.0)
SystemRequirements
Enhances
URL	https://www.lasseigne.org/
BugReports	https://github.com/lasseignelab/CoSIA/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	CoSIA_1.0.0.tar.gz
Windows Binary	CoSIA_1.0.0.zip
macOS Binary (x86_64)	CoSIA_1.0.0.tgz
macOS Binary (arm64)	CoSIA_1.0.0.tgz
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