SCENIC
An R package to infer gene regulatory networks and identify cell types from single-cell RNA-seq data.
What is SCENIC?
SCENIC is an R package that implements a computational method to infer gene regulatory networks and identify cell types from single-cell RNA-sequencing data. It solves the problem of understanding gene regulation at single-cell resolution by reconstructing transcription factor networks and clustering cells based on regulatory activity. The method is published in Nature Methods and supports multiple implementations for flexibility.
Bioinformaticians, computational biologists, and researchers analyzing single-cell RNA-seq data who need to infer regulatory networks and define cell types. It is suited for both exploratory analysis and large-scale studies.
Developers choose SCENIC for its established methodology, multi-platform support (R, Python, Nextflow), and comprehensive tutorials. Its integration with tools like SCope for visualization and scalability through distributed computing make it a robust choice for single-cell regulatory analysis.
Overview
SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
Use Cases
Best For
- Inferring transcription factor networks from single-cell RNA-seq data
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