---
pretty_name: Precancer-to-Tumor Progression Multi-omics (single-cell & spatial)
license: other
language:
- en
tags:
- biology
- medical
- cancer
- oncology
- single-cell
- scRNA-seq
- spatial-transcriptomics
- tumor-progression
- precancer
- multiomics
- genomics
viewer: false
size_categories:
- n>1T
---
# Precancer → Tumor → Late/Metastatic Progression Multi-omics

A curated, continuously-harvested collection of **publicly available** human multi-omics
datasets spanning the full tumor trajectory: **precancerous lesions → early carcinoma →
advanced / metastatic**. **Single-cell and spatial transcriptomics are prioritized.**

> ⚠️ **Provenance & licensing.** Every dataset here was downloaded from a **public,
> open-access** repository (no controlled-access or patient-identifiable data). Each dataset
> **retains the license and terms of its ORIGINAL source.** This repository is a research
> convenience mirror. **If you use any dataset, cite the original study and follow its
> license** — see the per-dataset manifest (`_catalog/`) for source, accession, URL, PMID/DOI.

## Contents (auto-updated 2026-06-23 08:20 UTC)
- **Datasets:** 3937  |  **Total size:** 706.7 GB
- **Single-cell:** 597  |  **Spatial:** 173  |  **Progression-series:** 1133
- **By source:** GEO 3513 · figshare 318 · cBioPortal 95 · CELLxGENE 93 · ArrayExpress 54 · SCEA 4 · UCSC-CellBrowser 1

### By modality
- other/unspecified: 1575
- bulk-RNA-seq: 673
- scRNA-seq: 544
- methylation: 441
- microarray: 237
- DNA-mutation: 196
- spatial-transcriptomics: 156
- proteomics-MS: 117
- bulk-ATAC: 69
- snRNA-seq: 45
- spatial-proteomics: 17
- scATAC: 8

## Repository structure
- `data/<SOURCE>/<ACCESSION>/` — processed / analysis-ready files per dataset
  (e.g. `.h5ad`, `matrix.mtx`+`barcodes`/`features`, Visium spatial matrices, count tables).
- `_catalog/precancer_catalog.csv` / `.xlsx` / `.parquet` — **full manifest**, one row per
  dataset: source, accession, modality, progression stage, size, source URL, PMID/DOI, summary.
- `_catalog/README.md` — human-readable running summary.

The `_catalog` manifest is the authoritative per-dataset metadata index.

## Sources
NCBI GEO · CZ CELLxGENE Discover · EBI Single Cell Expression Atlas · UCSC Cell Browser ·
HCA · figshare · Zenodo · cBioPortal · PRIDE · ArrayExpress/BioStudies. Each dataset's
license is that of its source repository / original publication.

## How to use
```python
from huggingface_hub import snapshot_download
p = snapshot_download("wei82/precancer-omics-data", repo_type="dataset",
                      allow_patterns=["_catalog/*", "data/CELLxGENE/*"])
# then load e.g. an .h5ad with scanpy / anndata, or matrix.mtx with scanpy.read_10x_mtx
```

## Related
Analysis outputs derived from these data are kept **private** at `wei82/precancer-omics-analysis`
(each result references the source dataset `uid` = `source:accession`).

## Disclaimer
Automatically harvested; not affiliated with the original data providers. Provided for
research convenience. Verify each dataset's original license before reuse or redistribution.