PT  - JOURNAL ARTICLE
AU  - Naim Al Mahi
AU  - Mehdi Fazel Najafabadi
AU  - Marcin Pilarczyk
AU  - Michal Kouril
AU  - Mario Medvedovic
TI  - GREIN: An interactive web platform for re-analyzing GEO RNA-seq data
AID  - 10.1101/326223
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 326223
4099  - http://biorxiv.org/content/early/2018/05/19/326223.short
4100  - http://biorxiv.org/content/early/2018/05/19/326223.full
AB  - The vast amount of RNA-seq data deposited in Gene Expression Omnibus (GEO) and Sequence Read Archive (SRA) is still a grossly underutilized resource for biomedical research. To remove technical roadblocks for re-using these data, we have developed a web-application GREIN (GEO RNA-seq Experiments Interactive Navigator) which provides simple user-friendly interfaces for manipulating and analyses of GEO RNA-seq data. GREIN is powered by the back-end computational pipeline for uniform processing of RNA-seq data and the large number (>5,500) of already processed datasets. The front-end user interfaces provide a wealth of user-analytics options including sub-setting and downloading processed data, interactive visualization, statistical power analyses, construction of differential gene expression signatures and their comprehensive functional characterization, connectivity analysis with LINCS L1000 data, etc. The combination of the massive amount of back-end data and front-end analytics options driven by user-friendly interfaces makes GREIN a unique open-source resource for re-using GEO RNA-seq data. GREIN is freely accessible at: https://shiny.ilincs.org/grein, the source code is available at: https://github.com/uc-bd2k/grein, and the Docker container is available at: https://hub.docker.com/r/ucbd2k/grein.Contact: Mario.Medvedovic{at}uc.edu