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. This information is provided as a service to the community and does not constitute an endorsement by the HCA.
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.
Bioconductor
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.
cellxgene
Chan Zuckerberg Initiative
cellxgene is an interactive, performant explorer for single cell transcriptomics data.
Cytoscape
Cytoscape consortium
Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways.
DNAstack
Cloud platform for bioinformatics based on open standards like Workflow Description Language and Common Workflow Language.
FASTGenomics
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.
GranatumX
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.
OmniBrowser™
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.
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.
Terra
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.
UCSC Xena
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.
