RT Journal Article
SR Electronic
T1 EGIDExpress: An Interactive Shiny Web App to Visualize and Share Large Biological Datasets
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2022.10.03.510709
DO 10.1101/2022.10.03.510709
A1 Besse, John A.
A1 Osswald, Garrett A.
A1 Ballaban, Adina Y.
A1 Caldwell, Julie M.
A1 Rothenberg, Marc E.
YR 2022
UL http://biorxiv.org/content/early/2022/10/07/2022.10.03.510709.abstract
AB Biomedical research on rare diseases faces challenges such as low availability of biological specimens to study and limited funding. Eosinophilic gastrointestinal diseases (EGIDs) are rare conditions associated with inappropriate inflammation and the accumulation of eosinophils in various segments of the gastrointestinal tract. We aimed to build a repository of large datasets related to EGIDs that would be easily browsable, interpretable, and accessible in order to facilitate data sharing and hypothesis generation. Using the R-code based package Shiny, we built a website that allows visualization of multiple types of datasets including microarray, RNAseq, protein array, single-cell RNAseq, and ChIPseq. Users can access EGIDExpress (https://egidexpress.research.cchmc.org/) to browse data on a per-gene basis and to generate graphic representation of the data. Additionally, users can download the processed data to initiate their own analyses. Within 34 months of launching EGIDExpress, over 2400 users from 37 countries and 37 states within the United States accessed the site. Overall, EGIDExpress is accelerating research on EGIDs and provides a prototypic platform for broad research data sharing.Competing Interest StatementThe authors have declared no competing interest.