Demonstration only. Corollary is a non-commercial research demo — no warranty, no support, not for commercial use or clinical decisions. Read the disclaimer

Corollary Labs
All models

Genomics & Single-Cell · VIB-KU Leuven

SCENIC+ / pySCENIC

Infers enhancer-driven gene regulatory networks from paired single-cell ATAC-seq and RNA-seq data.

Run it online

What SCENIC+ / pySCENIC is

SCENIC+ (and pySCENIC) is a genomics method developed by VIB-KU Leuven for gene regulatory network inference from single-cell profiling data.

The tool reconstructs enhancer-driven regulons, pinpointing which transcription factors govern specific target genes across distinct cell populations. By pairing single-cell chromatin accessibility with single-cell gene expression measurements, it produces mechanistic regulatory hypotheses rather than simple correlation patterns.

Key facts

Version
1.0
Domain
Genomics
Modalities
Single-cell RNA and single-cell ATAC
Hardware requirement
CPU

What you can use it for

Gene regulatory network inference
Deduce regulatory networks by linking transcription factors to downstream target genes across single cells.
Enhancer-driven regulon identification
Identify transcription factor regulons driven by enhancer activity using paired transcriptomic and chromatin accessibility profiles.
Cell-specific target gene mapping
Determine transcription factor activity and target gene sets associated with defined cell populations.

Run it here

No installation and no GPU of your own: fill in the inputs and it runs on our servers. Results stay in your browser unless you sign in.

Not runnable yet

This model isn't available to run right now.

Run this model

SCENIC+ / pySCENIC

Needs scrna matrix (h5ad url)

Strengths and limits

Good at

  • Reconstructs enhancer-driven regulons specifying transcription factors and their targets within individual cells.
  • Yields mechanistic regulatory hypotheses rather than simple statistical correlations.
  • Combines information from paired single-cell RNA-seq and single-cell ATAC-seq profiles.

Watch out for

  • Requires paired single-cell RNA and single-cell ATAC inputs supplied in h5ad format.
  • Involves significant computational demands to generate regulatory network hypotheses.

Inputs and outputs

You provide

  • scRNA matrix (h5ad URL)

  • scATAC matrix (h5ad URL)optional

You get back

  • TF → target regulons with enrichment scores.

Licence

Check the licence before commercial use · GPL-3.0

The GPL-3.0 licence carries terms worth reading before you depend on it.

Questions

Can I use SCENIC+ / pySCENIC commercially?

Check the licence before commercial use. The GPL-3.0 licence carries terms worth reading before you depend on it.

How do I run SCENIC+ / pySCENIC without installing anything?

Use the form under “Run it here” on this page: fill in the inputs and press Run model. It runs on our servers, typically in 2.0h, and a run costs about 16,800 credits. Visitors without an account get 1,000 credits a month.

What inputs does the tool require?

It accepts URLs pointing to single-cell RNA and single-cell ATAC matrices, both formatted as h5ad files.

What is the primary output?

It outputs a table of regulons detailing transcription factor to target relationships along with enrichment scores.

What hardware is necessary to run the tool?

The tool executes on standard CPU hardware.

Written from SCENIC+ / pySCENIC's own documentation. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.

Related models