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

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:

Documentation
Important Notes

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
[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 ~]$