nichecompass/gene_program_mask

Description

Generation of a prior knowledge gene program mask for NicheCompass.

Inputs

Name	Type & Properties	Description
--input_gene_orthologs_mapping_file	file	Path to a CSV file mapping human genes to mouse orthologs. Required for the OmniPath and NicheNet masks if `--species mouse`.
--input_metabolite_enzymes	file	Path to the MeBocost metabolite-enzymes TSV file. Required for generating the MeBocost gene program mask.
--input_metabolite_sensors	file	Path to the MeBocost metabolite-sensors TSV file. Required for generating the MeBocost gene program mask.
--input_omnipath_lr_network	file	Path to the OmniPath ligand-receptor network CSV file. If provided, the network will be loaded from this file instead of querying the OmniPath API. Cannot be used together with `--output_omnipath_lr_network`.
--input_nichenet_ligand_target_matrix	file	Path to the NicheNet ligand-target gene regulatory potential matrix file. If provided, the matrix will be loaded from this file instead of querying the NicheNet API.
--input_nichenet_lrt_network	file	Path to the NicheNet ligand-receptor network CSV file. If provided, the network will be loaded from this file instead of querying the NicheNet API.
--input_collectri_tf_network	file	Path to the CollecTRI TF-target gene regulatory network CSV file. If provided, the network will be loaded from this file instead of querying the CollecTRI API.

Name

Type & Properties

--input_gene_orthologs_mapping_file

file

--input_metabolite_enzymes

file

--input_metabolite_sensors

file

--input_omnipath_lr_network

file

--input_nichenet_ligand_target_matrix

file

--input_nichenet_lrt_network

file

--input_collectri_tf_network

file

Parameters

Name	Type & Properties	Description
--species	string	Species of the organism (human or mouse).
--create_omnipath_gene_program_mask	boolean	Whether to create the OmniPath gene program mask.
--create_nichenet_gene_program_mask	boolean	Whether to create the NicheNet gene program mask.
--create_mebocost_gene_program_mask	boolean	Whether to create the MeBocost gene program mask.
--create_collectri_tf_gene_program_mask	boolean	Whether to create the CollecTRI TF gene program mask.
--overlap_thresh_target_genes	double	The minimum ratio of target genes that need to overlap between a GP without source genes and another GP for the GP to be dropped. Gene programs with different source genes are never combined or dropped.

Name

Type & Properties

--species

string

--create_omnipath_gene_program_mask

boolean

--create_nichenet_gene_program_mask

boolean

--create_mebocost_gene_program_mask

boolean

--create_collectri_tf_gene_program_mask

boolean

--overlap_thresh_target_genes

double

Omnipath Parameters

Name	Type & Properties	Description
--omnipath_min_curation_effort	integer	Minimum number of times an interaction has to be described in a paper and mentioned in a database to be included in the OmniPath gene programs.

Name

Type & Properties

--omnipath_min_curation_effort

integer

NicheNet Parameters

Name	Type & Properties	Description
--nichenet_version	string	Version of the NicheNet ligand receptor network and ligand target gene regulatory potential matrix. `v2` is an improved version of `v1`, and has separate files for mouse and human.
--nichenet_keep_target_genes_ratio	double	Ratio of target genes that are kept compared to total target genes. This ratio is applied over the entire matrix (not on gene program level), and determines the `all_gps_score_keep_threshold`, which will be used to filter target genes according to their regulatory potential scores.
--nichenet_max_n_target_genes_per_gp	integer	Maximum number of target genes per gene program. If a gene program has more target genes than `max_n_target_genes_per_gp`, only the `max_n_target_genes_per_gp` gene programs with the highest regulatory potential scores will be kept. Default value is chosen based on MultiNicheNet specification (s. Browaeys, R. et al. MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data. bioRxiv (2023) doi:10.1101/2023.06.13.544751).

Name

Type & Properties

--nichenet_version

string

--nichenet_keep_target_genes_ratio

double

--nichenet_max_n_target_genes_per_gp

integer

Outputs

Name	Type & Properties	Description
--output	file required output	Path to the output gene program mask JSON file.
--output_omnipath_lr_network	file output	Path to the output OmniPath ligand-receptor network CSV file. If `--input_omnipath_lr_network` is not provided, the network will be saved to this file after querying the OmniPath API.
--output_nichenet_lrt_network	file output	Path to the output NicheNet ligand-receptor network CSV file. If `--input_nichenet_lrt_network` is not provided, the network will be saved to this file after querying the NicheNet API.
--output_nichenet_ligand_target_matrix	file output	Path to the output NicheNet ligand-target gene regulatory potential matrix file. If `--input_nichenet_ligand_target_matrix` is not provided, the matrix will be saved to this file after querying the NicheNet API.
--output_collectri_tf_network	file output	Path to the output CollecTRI TF-target gene regulatory potential network CSV file. If `--input_collectri_tf_network` is not provided, the network will be saved to this file after querying the CollecTRI API.
--output_omnipath_gp_gene_count_distributions	file output	Path to save the OmniPath gene program gene count distributions plot.
--output_nichenet_gp_gene_count_distributions	file output	Path to save the NicheNet gene program gene count distributions plot.
--output_mebocost_gp_gene_count_distributions	file output	Path to save the MeBocost gene program gene count distributions plot.
--output_collectri_tf_gp_gene_count_distributions	file output	Path to save the CollecTRI TF gene program gene count distributions plot.

Name

Type & Properties

--output

file

required

output

--output_omnipath_lr_network

file

output

--output_nichenet_lrt_network

file

output

--output_nichenet_ligand_target_matrix

file

output

--output_collectri_tf_network

file

output

--output_omnipath_gp_gene_count_distributions

file

output

--output_nichenet_gp_gene_count_distributions

file

output

--output_mebocost_gp_gene_count_distributions

file

output

--output_collectri_tf_gp_gene_count_distributions

file

output

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
species: [ "human" ]  
create_omnipath_gene_program_mask: [ true ]  
create_nichenet_gene_program_mask: [ true ]  
create_mebocost_gene_program_mask: [ true ]  
create_collectri_tf_gene_program_mask: [ true ]  
overlap_thresh_target_genes: [ 1 ]  
omnipath_min_curation_effort: [ 2 ]  
nichenet_version: [ "v2" ]  
nichenet_keep_target_genes_ratio: [ 1 ]  
nichenet_max_n_target_genes_per_gp: [ 250 ]  
output: "$id.$key.output.json"  
output_omnipath_lr_network: "$id.$key.output_omnipath_lr_network.csv"  
output_nichenet_lrt_network: "$id.$key.output_nichenet_lrt_network.csv"  
output_nichenet_ligand_target_matrix: "$id.$key.output_nichenet_ligand_target_matrix.csv"  
output_collectri_tf_network: "$id.$key.output_collectri_tf_network.csv"  
output_omnipath_gp_gene_count_distributions: "$id.$key.output_omnipath_gp_gene_count_distributions.svg"  
output_nichenet_gp_gene_count_distributions: "$id.$key.output_nichenet_gp_gene_count_distributions.svg"  
output_mebocost_gp_gene_count_distributions: "$id.$key.output_mebocost_gp_gene_count_distributions.svg"  
output_collectri_tf_gp_gene_count_distributions: "$id.$key.output_collectri_tf_gp_gene_count_distributions.svg"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline_spatial.git \  
  -revision v0.7.0 \  
  -main-script target/nextflow/nichecompass/gene_program_mask/main.nf \  
  -params-file params.yaml

nichecompass/gene_program_mask

Inputs

Parameters

Omnipath Parameters

NicheNet Parameters

Outputs

Run this component

Relationships

Used by

Uses