CoSIA
This is thereleased version of CoSIA; for the devel version, seeCoSIA.
An Investigation Across Different Species and Tissues
Bioconductor version: Release (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 [aut] ORCID: 0000-0002-1186-3114, Anthony B. Crumley [cre, aut] ORCID: 0009-0004-7347-4722, Nathaniel S. DeVoss [aut] ORCID: 0000-0003-0465-2770, Brittany N. Lasseigne [aut] ORCID: 0000-0002-1642-8904
Maintainer: Anthony B. Crumley <acrumley at uab.edu>
citation("CoSIA")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("CoSIA")For older versions of R, please refer to the appropriateBioconductor 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 |
Details
| biocViews | BiologicalQuestion,DataImport,GUI,GeneExpression,MultipleComparison,Software,ThirdPartyClient |
| Version | 1.10.1 |
| In Bioconductor since | BioC 3.17 (R-4.3) (2.5 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 |
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
FollowInstallation instructions to use this package in your R session.
| Source Package | CoSIA_1.10.1.tar.gz |
| Windows Binary (x86_64) | CoSIA_1.9.0.zip |
| macOS Binary (x86_64) | CoSIA_1.10.1.tgz |
| macOS Binary (arm64) | CoSIA_1.10.1.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 |