SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks

Quick Links

SCENIC+ is a new method for the inference of enhancer-driven gene regulatory networks (eGRN). It predicts genomic enhancers along with candidate upstream transcription factors (TF) and links these enhancers to candidate target genes. Specific TFs for each cell type or cell state are predicted based on the concordance of TF binding site accessibility, TF expression, and target gene expression.

References:

Carmen Bravo González-Blas, Seppe De Winter, Gert Hulselmans, Nikolai Hecker, Irina Matetovici, Valerie Christiaens, Suresh Poovathingal, Jasper Wouters, Sara Aibar & Stein Aerts
SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks
Nature Methods20, pages 1355–1367 (2023)

Documentation

Important Notes

Module Name: scenic-plus (see the modules page for more information)
Unusual environment variables set
- SCENIC_PLUS_HOME installation directory
- SCENIC_PLUS_BIN executable directory
- SCENIC_PLUS_DATA sample data directory

Interactive job

Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
[user@cn3144 ~]$ module load scenic-plus
Loading singularity  4.0.1  on cn1108
[+] Loading scenic-plus  1.0a1

Note that the scenic-plus application has been installed in a singularity container. The python executable accociated with the application is named "python-sp", in order to avoid confusion with the default "python" executable available on Biowulf:

[user@cn3144 ~]$ python-sp --version

Actually, all the executables available with this application are the links 
to the to the corresponding executables installed in the singularity container. 
[user@cn3144 ~]$ scenic-plus -h

usage: scenicplus [-h] {init_snakemake,prepare_data,grn_inference} ...

Single-Cell Enhancer-driven gene regulatory Network Inference and Clustering

positional arguments:
  {init_snakemake,prepare_data,grn_inference}

options:
  -h, --help            show this help message and exit

[user@cn3144 ~]$ scenic-plus init_snakemake -h
usage: scenicplus init_snakemake [-h] --out_dir OUT_DIR

Initialize snakemake pipeline

options:
  -h, --help         show this help message and exit
  --out_dir OUT_DIR  Path to out dir.

[user@cn3144 ~]$ scenic-plus prepare_data  -h
usage: scenicplus prepare_data [-h] {prepare_GEX_ACC,prepare_menr,download_genome_annotations,search_spance} ...

Prepare gene expression, chromatin accessibility and motif enrichment data.

positional arguments:
  {prepare_GEX_ACC,prepare_menr,download_genome_annotations,search_spance}

options:
  -h, --help            show this help message and exit

[user@cn3144 ~]$ scenic-plus grn_inference  -h
usage: scenicplus grn_inference [-h]
                                {TF_to_gene,region_to_gene,motif_enrichment_cistarget,motif_enrichment_dem,eGRN,AUCell,create_scplus_mudata}
                                ...

Infer Enhancer driven Gene Regulatory Networks.

positional arguments:
  {TF_to_gene,region_to_gene,motif_enrichment_cistarget,motif_enrichment_dem,eGRN,AUCell,create_scplus_mudata}

options:
  -h, --help            show this help message and exit




End the interactive session:
[user@cn3111 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$