Single-cell & spatial alternative processing atlas

scSpAS

An event-centric resource for exploring alternative splicing, polyadenylation and transcription start sites across cells, tissues and spatial contexts.

Examples: HNRNPH3, chr10:68337334-68337857:+, lung, cancer

2Species
37Tissues / organs
28Disease types
7Platforms
45Cell types
418,000+Cells
82,000+Spatial spots
123Datasets
2,500,000+Total events

Core Analysis Modules

Alternative Splicing Event Types

Browse

Spatial View

Current spatial observation

Select a spatial event

Choose a dataset, section, gene and event to inspect its spatial measurements.

Structure

Genomic structure

Selected event

Spatial Map Colored by Label

Spatial Map Colored by Event Usage

Spatial Map Colored by Host Gene Expression

Usage Across Spatial Regions

Host Gene Expression Across Spatial Regions

Event–Gene Expression Correlation

Genes must be detected in at least max(10 spots, 5% of matched spots) and show non-zero variance before Spearman correlation.

Event–Event Correlation

Rank other events by signed Spearman ρ (high to low); label the five strongest |ρ| values.

Cell View

Current dataset observation

Select an event

Choose a dataset, identification method and event to inspect its cell-level measurements.

Structure

Genomic structure

Selected event

UMAP Colored by Cell Types

UMAP Colored by Event Usage

UMAP Colored by Host Gene Expression

Usage Across Cell Types

Host Gene Expression Across Cell Types

Event–Gene Expression Correlation

Event–Event Correlation

Regulation

ATS regulatory genome browser

Add evidence tracks

Download

Sequence data catalog

Choose a dataset and data class

The catalog standardizes heterogeneous source files into four download classes. Click an available class inside a dataset card to download; classes with several files expand a compact chooser.

Dataset availability
Availability note. Files are indexed from datasets registered in dataset_metadata.xlsx. Downloads are provided one file at a time and are rate-limited during database review.

Help

About scSpAS

Overview

scSpAS is an event-centered atlas for alternative splicing (AS), alternative polyadenylation (APA) and alternative transcription start sites (ATS) in single-cell and spatial datasets.

Start from the Home search box or Browse page using a gene, event ID or genomic coordinate. Select an event row, then open its Cell, Spatial or Regulation view. The event context is retained when moving between compatible pages.

Quick route: Search → select an event → open an available analysis page → export results or source data.

Search & Browse

Search and Browse page overview
Search and Browse page.

The Home search and Browse search accept gene symbols/IDs, native event IDs, genomic coordinates and indexed biological terms. The expandable Batch search accepts up to 500 genes, event IDs or coordinates.

  1. Choose filters such as species, tissue, condition, data modality, technology and event type. Advanced filters contain method, dataset, sample and genome assembly.
  2. Click Apply Filters. Available choices update according to the current combination.
  3. Click a sortable column heading to reorder results, or use Previous, Next and Rows per page to navigate.
  4. Use the Cell, Spatial or Regulation button in the Open column to examine that exact event observation.
Continue with the same event: after selecting an event, use its Cell, Spatial or Regulation button to carry the same dataset, identification method and event into that analysis page. On an analysis page, the buttons beside the page title can continue the same event context to another compatible page.

A disabled Open button means that the corresponding evidence layer is unavailable for that dataset observation. Fresh Browse sessions initially show SE events.

Cell View

Cell View page overview
Cell View page.

Select a Dataset, identification Method, cell Annotation and Event, then click Apply Cell View. The page displays genomic structure, annotation UMAP, event usage, host-gene expression and group-level boxplots. Isoform panels appear only when isoform data are available.

In correlation sections, click Calculate to rank genes or events by Spearman correlation. Export downloads the full ranking. Selecting a target gene/event updates its UMAP and scatterplot.

The GSEA barplot uses the correlation-ranked gene list and WikiPathways: the x-axis is NES, and bar color can be switched between −log10(q value) and −log10(p value).

Spatial View

Spatial View page overview
Spatial View page.

Select a spatial Dataset, identification Method, grouping Label and Event, then click Apply Spatial View. Region annotation is used by default when available.

The three main maps show label, event usage and host-gene expression on matched tissue coordinates. Regional boxplots summarize the same values by the selected label; optional isoform maps appear when available.

Event–gene correlation, GSEA, target-gene selection, event–event correlation and export work in the same way as in Cell View, but use matched spatial spots.

Regulation

Regulation page overview
Regulation page.

Select the dataset, method, annotation and event, then click Apply Regulation. All tracks are aligned to the same genomic ruler and automatically match the event species and assembly.

AS / APACell-type coverage, CLIP-seq, ESE/ESS motifs, PTM sites, protein domains, CpG islands and conservation.
ATSCell-type coverage, CAGE-seq, ATAC-seq, histone marks, CpG islands and conservation.

Click an evidence button to show or hide its track; expandable buttons allow individual tracks to be selected. Use arrows to pan, +/− to zoom, Reset to restore the locus and Track order to rearrange active groups. Hover over features for labels and coordinates.

CLIP peaks additionally report RBP/sample metadata and log10 p.value. The candidate RBP table can be sorted by its numeric columns.

Data access

Download

Filter files by data modality, technology, species, condition, event type, dataset or file category, then click Apply. Reset clears all filters. Dataset cards summarize availability and provide direct file downloads.

Standard categories are event matrices, normalized gene-expression matrices, isoform matrices and cell/spot metadata. Not every dataset contains every category.

Interpretation

Notes

0 versus NA0 is a measured zero; NA/gray means no valid measurement and is not treated as zero.
Unavailable contentA disabled button or hidden optional panel means that compatible source data are absent for the selected observation.

If a search returns no records, clear filters and verify the method-specific event ID. For data problems, include the dataset, method, complete event ID and genome assembly when contacting the team.

Contact

Author Affiliation

1 Department of Laboratory Medicine, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University, Chengdu 610041, China

2 Biosafety Laboratory of West China Hospital, Center for Biological and Translational Research, West China Hospital, Sichuan University, Chengdu, 610041, China

Citation

If you use scSpAS in your research, please cite:

Chen, L., Liu, D., He, Z., Xu, Z., Lin, J.-w. & Chen, L. scSpAS: an integrated single-cell and spatial atlas of transcript isoform regulation. Version 1.0 (2026).