SCENIC
SCENIC+ for combined single cell chromatin accessibility and gene expression. SCENIC+ is a tool which takes combined single-cell crhomatin accessibility and gene expression data as input to infere enhancer-drive gene regulatory networks.
SCENIC: single-cell regulatory network inference and clustering
2017年10月9日 · SCENIC enables simultaneous regulatory network inference and robust cell clustering from single-cell RNA-seq data. We present SCENIC, a computational method for simultaneous gene regulatory...
SCENIC+: single-cell multiomic inference of enhancers and gene …
2023年7月13日 · Here, we developed SCENIC+, a computational framework that combines single-cell chromatin accessibility and gene expression data with motif discovery to infer enhancer-driven GRNs (eGRNs).
SCENIC is an R package to infer Gene Regulatory Networks and cell …
2021年3月26日 · SCENIC (Single-Cell rEgulatory Network Inference and Clustering) is a computational method to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data. The description of the method and some usage examples are available in …
SCENIC: single-cell regulatory network inference and clustering
On a compendium of single-cell data from tumors and brain, we demonstrate that cis-regulatory analysis can be exploited to guide the identification of transcription factors and cell states. SCENIC provides critical biological insights into the mechanisms driving cellular heterogeneity.
called SCENIC (Single-Cell rEgulatory Network Inference and Clustering), to map GRNs, and then identify stable cellular states by evaluating the activity of the GRNs in each cell. The SCENIC workflow consists of three steps (Fig. 1a, Supplementary Fig. 1 and Online Methods).
A scalable SCENIC workflow for single-cell gene regulatory …
2020年6月19日 · This protocol explains how to perform a fast SCENIC analysis alongside standard best practices steps on single-cell RNA-sequencing data using software containers and Nextflow pipelines.
SCENIC (Single-Cell rEgulatory Network Inference and Clustering) …
Starting with single cell gene expression data, we offer as a service the SCENIC protocol, both in R and Python (on ACCRE or AWS). SCENIC and pySCENIC consist of a shared computational method for simultaneous gene regulatory network reconstruction and cell-state identification from single-cell RNA-seq data ( Aibar et al, 2017 , Van de Sande et ...
SCENIC: single-cell regulatory network inference and clustering
We present SCENIC, a computational method for simultaneous gene regulatory network reconstruction and cell-state identification from single-cell RNA-seq data (http://scenic.aertslab.org ).
Tutorials - SCENIC
SCENIC+ analysis on non-multiome data: separate scATAC-seq and scRNA-seq on different cells of the same sample; Transcription factor perturbation simulation; Unbranched GRN velocity; Branched GRN velocity
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