Analysis Tools Registry

Analysis Portals

Analysis portals listed below provide a human-friendly UI in a web or native app to search and explore biological data. Portals sometimes include packages for analysis methods and biological visualizations, and integrate data from Human Cell Atlas.

These solutions are built by third parties, and fostered by the HCA DCP.

Are you developing a portal that can consume HCA data? Please submit it for inclusion in the registry.

Automated Single cell Analysis Platform (ASAP)

Vincent Gardeux, Fabrice David, Bart Deplancke

ASAP allows the user to perform custom analyses and compare algorithms for each step of the single cell or bulk RNA-seq analysis pipeline post genome alignment.

BioTuring Browser

BioTuring Team

BioTuring Single Cell Browser combines modern data visualization techniques, statistical machine learning toolboxes, and a rich knowledge base to create a unique platform for single cell data analytics.


Chan Zuckerberg Initiative

cellxgene is an interactive, performant explorer for single cell transcriptomics data.


Cytoscape consortium

Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways.


Cloud platform for bioinformatics based on open standards like Workflow Description Language and Common Workflow Language.

Human Cell Atlas Galaxy Instance

P Moreno, N Huang, J Manning, S Mohammed, C Talavera-Lopez, K Polanski, W Bacon, B Gruening, H Rasche, K Meyer, S Teichmann, A Brazma, I Papatheodorou

The Human Cell Atlas Galaxy instance contains tools for Single Cell analysis and interactive visualisation (UCSC CellBrowser). It can import matrix data from the Human Cell Atlas and the EBI Single Cell Expression Atlas, for re-analysis.

Single Cell Expression Atlas

Gene Expression Team at EMBL-EBI, Irene Papatheodorou

Single Cell Expression Atlas supports research in single cell transcriptomics.

Single Cell Portal

Jon Bistline, Eric Weitz, Jean Chang, Vicky Horst, Timothy Tickle

Single Cell Portal (SCP) provides interactive visualizations, easy-to-run cloud scalable workflows and analyses, and secure sharing permissions that support all stages of scientific inquiry.

The GenePattern Notebook Environment

Mesirov lab, UCSD

GenePattern Notebook integrates the popular Jupyter Notebook platform, which interleaves text, graphics, and code, with the hundreds of genomic analyses available in the GenePattern platform.

UCSC Cell Browser

Max Haeussler

UCSC Cell Browser is a software tool for single cell RNA expression.


Brian Craft, Mary Goldman, Jingchun Zhu, David Haussler

UCSC Xena is an online exploration tool for multi-omic functional genomics data and associated meta-data and annotations.

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