CoSIA
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
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("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
| Reference Manual |
Details
| biocViews | BiologicalQuestion, DataImport, GUI, GeneExpression, MultipleComparison, Software, ThirdPartyClient |
| Version | 1.3.1 |
| 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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| Depends On Me | |
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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 | |
| 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 |