ASE table
Donor-controlled allelic-balance results.
Download TSVscTHREAD: a uniformly reprocessed single-cell long-read transcriptome resource
scTHREAD integrates 67 Oxford Nanopore single-cell long-read samples and reconstructs each dataset from raw reads through one IsoQuant workflow. The shared read-level evidence layer resolves transcript class, splice chain and per-cell UMI support, enabling comparable analyses of isoform usage, poly(A) site choice, allelic balance and recurrent novel junctions. Genome Biology resource
Statistics
67
Samples / runs
—
Cells
—
Observed isoforms
67 samples, uniformly reprocessed
Loading biological study descriptions…
Global cell map
Loading the 67-sample UMAP…
All 67 samples/runs. UMAP is exploratory and does not imply trajectory.
Database coverage
Read facts
67 / 67
Isoform
66 / 67
Poly(A)
67 / 67
ASE
62 / 67
Junction
66 / 67
Known source gaps are retained as missing values and are not imputed.
Transcript & junction browser interactive
Choose a gene to load expression, DIU, APA, ASE and junction evidence.
Scroll over the track to zoom · drag horizontally to pan · select an arc or table row for details.
| Junction | Span | Molecules | Reads | Runs | Studies |
|---|
Cell-type annotation
Gene expression
Validated 67-sample embedding from long-read gene expression with run-aware integration. UMAP is exploratory and does not imply trajectory.
Live data scope: queries run against the completed 66-sample junction aggregation. Results are aggregated on demand and bounded to a 5 Mb window.
Search scTHREAD
Search studies, genes, junctions and genomic regions through the scTHREAD API.
Analyze
Compare evidence across cell types.
Choose a gene or junction, then select from cell-type pairs supported by enough paired biological samples. Ineligible combinations are not shown.
Analyzed
Your comparison will appear here
Results include paired effect sizes, biological-unit counts and exact eligibility boundaries. Unsupported inference is withheld.
Model prediction
Estimate pooled junction usage where observation is incomplete.
Predict v1 is cell-type agnostic. Predictions complement observed evidence; they never replace it, and every response reports validation, applicability and uncertainty.
Checking whether a validated model is available…
Predicted
No prediction requested
A validated model may abstain when a junction falls outside its training domain.
Database annotation
Annotate junctions against scTHREAD evidence.
Normalize coordinates and retrieve deterministic motif, recurrence, coverage and sequence/RBP annotations for one junction or a batch.
Ready to annotate
Unmatched and invalid coordinates remain explicit in the output.
Uniform processing workflow
Raw ONT reads
Study-level sequencing runs enter without relying on published aggregates.
IsoQuant
FSM, ISM, NIC and NNC classification with splice-chain reconstruction.
Cell × molecule
Run-aware barcode joins and per-cell UMI deduplication.
Shared evidence
Isoform, PAS, junction and allelic views from one read-facts layer.
Show processing details
Long-read alignments and IsoQuant assignments are harmonized within each run. Gene, transcript, poly(A)-site, junction and allelic evidence use run-aware barcode namespaces; UMI deduplication is applied where molecule tags are available.
Show analysis details
On-demand comparisons merge technical runs into registered biological sample or capture units. The interface offers only cell-type pairs supported by at least three shared units. Allelic balance remains descriptive because haplotype labels are not phased consistently across units.
Download
Sample manifest
One row per sequencing run, with biological context, source accessions, platform and processed-cell count.
| Study | Biological context | Run accession | Species | Platform | Library kit | Cells |
|---|---|---|---|---|---|---|
| Loading sample-level metadata… | ||||||
About scTHREAD
Loading release metadata from the backend…