Human Cell Atlas Data Coordination Platform
Analysis Tools 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.


Bioconductor organization

Bioconductor provides more than 2100 R packages for the statistical analysis, comprehension, and visualization of high-throughput genomic data.

BioTuring Browser

BioTuring Team

BioTuring 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.

Cambridge Cell Atlas

Wellcome Sanger Institute, European Bioinformatics Institute

Analysis, visualisation and tools for exploration of single cell RNA-Seq data generated by the Human Cell Atlas initiative, as well as other projects on human tissue.


Cellenics® software was developed by © 2020-2022 President and Fellows of Harvard College. Biomage is an open source software company that provided services to Harvard Medical School for the design and development of Cellenics®.

Cellenics® is an open source, cloud-based analytics tool for single-cell RNA sequencing data that that has been developed at Harvard Medical School.


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.


Comma Soft AG

FASTGenomics is a platform to share scRNA-seq data and analyses. Users can either choose from best practices or create individual workflows for the exploration of gene expression data.

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.


Lana Garmire, David Garmire, Xun Zhu et al.

GranatumX is a next-generation software environment for single-cell data analysis. GranatumX is inspired by the interactive web tool Granatum (published in Genome Medicine, 2017). It enables biologists to flexibly design their own pipelines for single-cell analysis in a web-based graphical environment.

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.


Abiosciences Team

OmniBrowser™ is a comprehensive curated single cell data compendium with visualization and analysis capabilities that further empower and innovate drug discovery and development.

Polly by Elucidata


Polly is a data-ops platform that provides access to ~50,000 curated bulk and single-cell RNA-seq datasets, facilitating rapid detection of drug targets and biomarkers across diseases.

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.

SynEcoSys single-cell RNA sequencing database

Singleron Technologies

SynEcoSys is a multifunctional platform for single-cell transcriptomic data analysis, visualization, and exploration. SynEcoSys curates both clinical and research orientated data to regard disease related cells and genes.


Broad Institute, Microsoft, and Verily

Terra is a secure, scalable, open-source platform for biomedical researchers to access data, run analysis tools and collaborate.

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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