Data Resources
CELLxGENE, Human Cell Atlas, GEO, SRA, Single Cell Portal, Tabula Sapiens, Allen resources, and domain-specific databases like PanglaoDB and TISCH2.
Single-cell omics portal
Single Cell Hub
A living portal for single-cell and spatial omics: atlases, tools, workflows, benchmarks, and the signals worth tracking next.
Why it exists
Single-cell work has become a navigation problem.
The field now moves through massive atlases, multimodal assays, spatial platforms, pretrained models, and many overlapping analysis ecosystems. The hub brings selected, reviewed starting points into a searchable, source-linked resource layer.
Portal architecture
A source-linked map of the single-cell landscape.
Each resource carries practical context: tags, source links, modality support, update signals, and curator notes that help users decide where to go next.
Tools Catalog
Seurat, Scanpy, scverse, scvi-tools, Harmony, Squidpy, Open Problems tasks, and specialized spatial or multimodal methods like Muon, MOFA+, and GLUE, plus Illumina Connected Multiomics for commercial multiomics and spatial analysis.
Workflows
Practical paths through single-cell best practices, OSCA, Seurat tutorials, and Scanpy tutorials.
Signals Feed
Watch scverse updates, CELLxGENE Census, Open Problems, and new spatial, multimodal, and AI methods.
01 / Data Resources
Selected reference portals, archives, and atlases worth checking first.
A seed catalog for dataset discovery, raw-data retrieval, atlas reuse, disease context, markers, and spatial or multimodal reference work. Suggestions help the map grow without pretending it is already exhaustive.
02 / Tools Catalog
Selected analysis ecosystems, methods, registries, and practical interfaces.
This seed catalog connects each entry to its primary source and tags it by workflow role, language, modality, and practical use.
Workflows
Make the next analysis step obvious.
Workflow pages connect practical decisions to trusted references: what to run, when to use it, and which assumptions to check before interpreting results.
First scRNA-seq analysis
QC, normalization, feature selection, dimensional reduction, clustering, marker genes, and reproducible reporting.
Single-cell best practicesAtlas reuse and integration
Dataset discovery, metadata review, label transfer, batch-aware integration, reference mapping, and biological conservation.
Seurat integration guideSpatial and multimodal
RNA plus ATAC, protein, perturbation, tissue context, neighborhood analysis, and modality-aware method selection.
Spatial best-practice topicsBenchmarks
Separate popularity from evidence.
Benchmark summaries focus on robustness, scalability, biological conservation, integration behavior, and modality support.
Question
Signal
Evidence
Can it scale?
Cells, memory, runtime
Benchmarks, docs, reports
Where does it fit?
Assay, species, workflow stage
Curator notes, examples
Signals Feed
Follow releases, papers, benchmarks, and methods that shape the field.
The feed collects source channels and watch areas for releases, benchmarks, preprints, methods, and field-level shifts.
Package releases and ecosystem notes
Watch scverse, Seurat, scvi-tools, CELLxGENE, and core package release notes for breaking changes, new tutorials, and API shifts.
Evidence over popularity
Track benchmark tasks, leaderboards, and comparison papers for integration, annotation, multimodal translation, scalability, and biological conservation.
Preprints and method papers
Follow new spatial, multimodal, perturbation, and AI/foundation model work, then promote only validated resources into the main catalog.
Spatial, multimodal, and AI directions
Watch for single-cell resolution spatial platforms, paired and unpaired multi-omics integration, perturbation prediction, and reusable pretrained model hubs.
About us
An independent resource for the single-cell community.
Single Cell Hub is a community-led project designed to make single-cell and spatial omics easier to navigate. We curate a practical, source-linked map of datasets, tools, workflows, benchmarks, and emerging methods for researchers, educators, and builders.
The project is contributor-supported and centers on careful curation, lightweight review, and transparent source links. Contributors can help by checking links, suggesting resources, improving summaries, writing workflow notes, or reviewing new submissions.
Contribute
Contributor interest
Share how you would like to help with curation, writing, review, design, or engineering. Contributor notes open as an email draft so the project team can review them alongside resource updates.
Community
Community review keeps the map useful.
Resource suggestions, contributor notes, and curator review form the feedback layer around the catalog. The goal is to keep entries accurate, source-linked, and useful to working researchers.
Curation principles
How resources earn attention here.
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Source-linked
Every entry points to an official page, primary documentation, repository, or recognized portal.
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Useful context
Tags describe modality, species, workflow role, platform, interface, and practical use.
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Evidence-aware
Benchmarks, method papers, and community standards are surfaced beside popularity signals.
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Reviewed
Contributor notes and resource suggestions help keep summaries accurate as the field changes.
Contributor pathways
Ways to strengthen the hub.
Resource curation
Suggest high-value datasets, portals, tools, and tutorials with primary links and short context.
Workflow notes
Contribute practical analysis paths for QC, integration, annotation, spatial, and multimodal work.
Tool review
Help evaluate maintenance status, documentation quality, scalability, and modality support.
Signal watching
Track releases, benchmark updates, preprints, and emerging spatial or AI-driven methods.