CoSIAdata

ExperimentHub package for CoSIA: 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 Coefficient of Variation and Shannon Entropy based Diversity 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 across the tissues and genes of five commonly used biomedical research species (Mus musculus, Rattus norvegicus, Danio rerio, Drosophila melanogaster, and Caenorhabditis elegans) in addition to Homo sapiens.

Getting Started

Installing

In preparation for the Bioconductor 3.17 release, we have developed CoSIA within a Bioconductor docker. Follow the instructions on Bioconductor's Docker Help Page to install and run CoSIAdata within the bioconductor_docker:devel container.

In R:

## Install BiocManager if necessary; Install CoSIAdata
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("CoSIAdata")
library(CoSIAdata)

Using CoSIAdata

CoSIAdata has species-specific helper functions for accessing expression data

c_elegans_vst_counts <- CoSIAdata::Caenorhabditis_elegans()

Check out the vignette for more information on accesssing specific data in CoSIAdata.

Authors

• Anisha Haldar
• Vishal H. Oza
• Nathaniel DeVoss
• Amanda D. Clark
• Brittany N. Lasseigne

Lasseigne Lab

What is Happening in the Lasseigne Lab?

Funding

This work was supported in part by the UAB Lasseigne Lab Start-Up funds (BNL, AH, ND, ADC and VHO), the UAB Pilot Center for Precision Animal Modeling (C-PAM) (1U54OD030167) (BNL and VHO), UAB Pilot Center for Precision Animal Modeling (C-PAM) - Diversity Supplement (3U54OD030167-03S1) (ADC), and Mentored Experiences in Research, Instruction, and Teaching (MERIT) Program (K12 GM088010) (ADC).

Acknowledgements

The authors would like to thank the members of the Lassigne lab for their support and feedback, in particular, Elizabeth J. Wilk, Jordan Whitlock, and Timothy C. Howton.

License

This project is licensed under the MIT License - see the LICENSE.md file for details