#12 · Tools & infrastructure
Curated portals, databases and workflows consolidate spatial and single-cell data for…
The dominant thread is infrastructure that consolidates heterogeneous spatial and single-cell data and standardizes access to it. HuBMAP Data Portal offers search and visualization across 9,316 public datasets from healthy human tissues. STRAND harmonizes 35 subcellular-resolution spatial transcriptomics datasets comprising about 4.9 billion transcript coordinates. SpaceBlocks, a Snakemake workflow, targets reproducible, expert-supervised cohort-level analysis of single-cell-resolution spatial data. Pycea and TreeData bring lineage trees into scverse/Scanpy-compatible analysis. SENgEAR, PathoEvo and CircaVal apply interactive database and web-platform approaches to senescence, disease progression and circadian regulation, though they are less specifically spatial. The contribution is integration and access rather than new inference methods.
Published papers
HuBMAP Data Portal: a resource for multimodal spatial and single-cell data of healthy human tissues.
HuBMAP Data Portal hosts 9,316 public spatial and single-cell datasets from healthy human tissues, with search and visualization tools.
STRAND: a comprehensive subcellular-resolved spatial transcriptome RNA architecture and navigation database.
STRAND is a curated database and analysis platform harmonizing 35 subcellular-resolution spatial transcriptomics datasets (~4.9 billion transcript coordinates)…
PathoEvo: an interactive single-cell database for exploring disease progression and pathological evolution.
Disease progression is driven by coordinated changes in tissue microenvironments, cellular composition, cell states, and transcriptional programmes.
CircaVal: a gene-centric multi-omics platform for exploring circadian regulatory features.
CircaVal is a gene-centric multi-omics database and web platform integrating public circadian datasets across humans, mice, and baboons, with an integrated…
Preprints
SpaceBlocks: an expert-supervised workflow for cohort-level spatial transcriptomics analysis
SpaceBlocks is a Snakemake workflow for reproducible, expert-supervised cohort-level analysis of single-cell-resolution spatial transcriptomics across Visium…
Pycea: a scverse toolkit for single-cell lineage tracing analysis
Pycea, a Python toolkit, and TreeData, an AnnData extension, integrate lineage trees with single-cell measurements for scverse/Scanpy-compatible lineage…
SENgEAR: an interactive visualization platform for comparative analysis of senescence signatures and cellular communication
SENgEAR is a no-code web platform for annotating senescent cells, visualizing cell-cell communication, and comparing senescence signatures across datasets and…
Topic history
| Date | Rank |
|---|---|
| #12 | |
| #6 | |
| #4 | |
| #1 | |
| #1 | |
| #1 | |
| #4 | |
| #15 | |
| #6 | |
| #18 | |
| #8 | |
| #33 | |
| #38 | |
| #32 | |
| #33 | |
| #37 |