Data
Dataset records, tissue sources, cell numbers, platforms, publications, and download links.
Maize single-cell resource
scMaize Single-cell atlas and foundation model
A curated maize single-cell resource for atlas visualization, gene expression query, model access, and data download.
Integrated UMAP
Color by cell type
20+Projects
385,675Cells
66Samples
7Tissues
3Platforms
Resources
Database modules
Atlas
Integrated UMAP, tissue distribution, cell type annotation, and marker gene expression.
Models
scMaize model versions, pretrained weights, and evaluation results.
Apps
Annotation, embedding extraction, expression imputation, and gene similarity tools for query datasets.
Download
Expression matrices, metadata, integrated embeddings, model weights, and example files.
Help
Quick start, atlas guide, model guide, citation, FAQ, and contact information.
Data Resources
Integrated maize single-cell and single-nucleus transcriptomic datasets.
20+Projects
385,675Cells
66Samples
7Tissues
3Platforms
Tissue coverage
Dataset summary
SourcePublic datasets
Data typesc/snRNA-seq
OutputMatrix / Metadata / Embedding
| Project | Tissue | Samples | Platform | Publication | Resource |
|---|---|---|---|---|---|
| Loading... | |||||
scMaizeAtlas
Interactive maize single-cell atlas with tissue, cell type, and gene expression layers.
Interactive visualizationIntegrated UMAP
Color: Cell type
Loading atlas data...
Loading model performance...
Online Apps
Submit maize single-cell query data to scMaize tools, track asynchronous jobs, and retrieve result files from a private status link.
Run scMaize analyses without local setup
The Apps portal accepts query files, places jobs into a shared queue, and returns a status link for each submission. Results can be downloaded after the job finishes.
Use the dedicated Apps portal for uploads, job tracking, and result download. The main database page remains focused on browsing atlas resources.
Launch SCmaize AppsCell Type Annotation
Predict tissue and cell type labels for query maize single-cell or single-nucleus expression data using the scMaize reference atlas.
Open annotation toolCell Embedding
Extract 384-dimensional scMaize cell representations for downstream visualization, clustering, retrieval, or model-based comparison.
Open embedding toolExpression Imputation
Estimate missing or sparse gene expression values with gene-neighbor relationships learned by the scMaize model.
Open imputation toolGene Similarity
Search functionally similar maize genes from the scMaize gene embedding space using one or more query gene symbols.
Open similarity toolDownload
Data files, model weights, embeddings, and example datasets.
Loading resources Reading the database file index
Help
Guide, citation, and contact information.
Quick start
Use Data to browse projects, samples, tissues, platforms, publications, and linked source records. Open Atlas for UMAP exploration, Models for pretrained model resources, and Download for metadata, H5AD, model weights, reports, RDS files, and expression matrices.
Data guide
Search by project, sample, tissue, PubMed, or platform. Open a project row to view sample-level metadata, source links, and available files. Dataset filters can be combined for narrower browsing.
Atlas guide
The Atlas page shows a lightweight UMAP preview generated from the integrated scMaizeAtlas. Color points by cell type, major cell type, tissue, project, or variety, and use filters to focus on selected tissues, cell types, or projects.
Models guide
The Models page summarizes scMaizeExp and scMaizeGO resources. Performance values are synchronized daily from the project GitHub README.
Download guide
Use Download for global resources such as metadata, atlas H5AD, and model weights. For sample-specific files, open the Data detail modal and download raw matrices, reports, or filtered RDS files from each sample.
Citation
Please cite scMaize when using atlas data, embeddings, model weights, or derived results. Until a formal citation is listed, link to the project repository: yjthu/scMaize.
Contact us
For data, model, or website questions, use the protected email link below or open the project repository.