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 (3.21)

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: ), Vishal H. Oza [aut] (ORCID: ), Amanda D. Clark [cre, aut] (ORCID: ), Nathaniel S. DeVoss [aut] (ORCID: ), Brittany N. Lasseigne [aut] (ORCID: )

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


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	BiologicalQuestion, DataImport, GUI, GeneExpression, MultipleComparison, Software, ThirdPartyClient
Version	1.7.0
In Bioconductor since	BioC 3.17 (R-4.3) (1.5 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

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
Windows Binary (x86_64)
macOS Binary (x86_64)
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
Package Short Url	https://bioconductor.org/packages/CoSIA/
Package Downloads Report	Download Stats