News and events from BioInfoRx and the communities
June 15, 2022

News: CellDepot: A Game-Changing Platform for Exploring and Comparing Single-Cell RNA-seq Data

BioInfoRx with collaboration with Biogen, has released CellDepot, a unified repository for scRNA-seq Data and visual exploration. The work is published in the Journal of Molecular Biology.

The exponential growth in scRNA-seq datasets has led to the urgent need to build a centralized space for managing, analyzing, and visualizing them to yield comprehensive insights from this big data. Although several tools and databases have been built to store, analyze, and visualize scRNA-seq datasets, CellDepot offers unique features that differentiate it from other portals. For instance, it is the only platform supporting joint conditional statements through graphical user interface, and  its unique visualization plugin has more features than most other tools. Scientists can now explore single-cell RNA sequencing (scRNA-seq) datasets and compare them across various studies with the help of CellDepot. The web application contains hundreds datasets from multiple species and tissues, and offers a user-friendly interface with advanced visualization and analytical capabilities.

The platform also embeds the cellxgene VIP tool, which enables fast exploration of individual datasets in an interactive and scalable manner. Cellxgene VIP offers more than 20 frequently applied plotting functions and high-level analysis methods, making it easier for scientists to gain more refined insights into cell composition, gene expression profiles, and differentially expressed genes among cell types or treatments.

CellDepot is a game-changer in the field of scRNA-seq, offering a unique and comprehensive platform for managing, analyzing, and visualizing single-cell datasets. With its advanced visualization and analytical capabilities, the platform is expected to empower scientists and bioinformaticians to explore, visualize, and compare scRNA-seq datasets in a collaborative manner, leading to better insights and discoveries in the field.

CellDepot is open-source software released under the MIT license, which motivates crowd contribution, broad adoption, and local deployment for private datasets. The web portal containing hundreds single-cell datasets is freely available at

For researchers who require expert support for managing their private single-cell datasets and advanced visualization using cellxgene VIP,  BioInfoRx offers scRNA-Seq data management services through the BxGenomics product