An intuitive and scalable web-portal for the standardized analysis of scRNA-seq data.

Description: CReSCENT, the CanceR Single Cell ExpressioN Toolkit (, is an intuitive and scalable web portal incorporating a containerized pipeline execution engine for standardized analysis of single-cell RNA-seq (scRNA-seq) data. While scRNA-seq data for cancer specimens are easily generated, subsequent analysis requires high-performance computing infrastructure and user-expertise to tailor interpretation for cancer. CReSCENT is populated with multiple public data sets and preconfigured pipelines that are user-editable to allow for optimization, comparison, and reanalysis on the fly. CReSCENT outputs interactive t-SNE, UMAP, and violin plots, allowing users to rapidly filter genes of interest without having to re-run the pipeline. In addition, plots, tables and R objects are downloadable through the user interface for offline analysis. The workflow is open-source and available at

Authors: Suluxan Mohanraj, Javier Diaz-Mejia, Martin Pham, Hillary Elrick, Shaikh Rashid, Prabnur Bal, Kevin Lu, Ping Luo, Alaina Mahalanabis, Alaine Naidas, Parisa Shooshtari, Arun Ramani, Michael Brudno, Trevor J. Pugh
Lab: Pugh
Version: 1
Keywords: CReSCENT, scRNA-seq, datasets, pipeline, visualization, R
Licensing: MIT License


Mohanraj, S., Diaz-Mejia, J. J., Pham, M., Elrick, H., Husic, M., Rashid, S., ... & Mahalanabis, A. (2020). CReSCENT: CanceR Single Cell ExpressioN Toolkit. bioRxiv.