feature_annotation/score_genes_scanpy

Description

Calculates the score of a set of genes for each cell, as implemented by scanpy.
The score is the average expression of a set of genes subtracted with the average expression of a reference set of genes.

Type

python_script

License

MIT

Links

Repository

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
modality: [ "rna" ]  
output: "$id.$key.output.h5mu"  
obs_score: [ "score" ]  
ctrl_size: [ 50 ]  
n_bins: [ 25 ]  
random_state: [ 0 ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v4.0.0 \  
  -main-script target/nextflow/feature_annotation/score_genes_scanpy/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--input	file required	Input h5mu file
--gene_list	string multiple	List of gene symbols to be scored.
--gene_list_file	file	Path to a .txt file containing the gene list to be scored. The gene list file should be formatted as a single column with gene symbols.
--gene_pool	string multiple	List of gene symbols for sampling the reference set. Default is all genes.
--gene_pool_file	file	File with genes for sampling the reference set. Default is all genes. The gene pool file should be formatted as a single column with gene symbols.
--modality	string	Which modality from the input MuData file to process.
--input_layer	string	The layer of the adata object containing normalized expression values. If not provided, the X attribute of the adata object will be used.
--var_gene_names	string	.var column name to be used to detect mitochondrial genes instead of .var_names (default if not set).
--allow_missing_genes	boolean	Whether to run score_genes when some genes in the gene_list or gene_list_file are not present in the gene_pool

Name

Type & Properties

--input

file

required

--gene_list

string

multiple

--gene_list_file

file

--gene_pool

string

multiple

--gene_pool_file

file

--modality

string

--input_layer

string

--var_gene_names

string

--allow_missing_genes

boolean

Outputs

Name	Type & Properties	Description
--output	file required output	Output h5mu file
--obs_score	string	Name of the score field to be added in .obs.
--output_compression	string	Compression format to use for the output AnnData and/or Mudata objects. By default no compression is applied.

Name

Type & Properties

--output

file

required

output

--obs_score

string

--output_compression

string

Arguments

Name	Type & Properties	Description
--ctrl_size	integer	Number of reference genes to be sampled from each bin. If len(gene_list) is not too low, you can set ctrl_size=len(gene_list).
--n_bins	integer	Number of expression level bins for sampling.
--random_state	integer	The random seed for sampling.

Name

Type & Properties

--ctrl_size

integer

--n_bins

integer

--random_state

integer