feature_annotation/score_genes_cell_cycle_scanpy

Description

Calculates the score associated to S phase and G2M phase and annotates the cell cycle phase 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.

Inputs

Name	Type & Properties	Description
--input	file required	Input h5mu file
--modality	string
--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	The name of the column in the var attribute of the adata object that contains the gene names (symbols). If not provided, the index of the var attribute will be used.

Name

Type & Properties

--input

file

required

--modality

string

--input_layer

string

--var_gene_names

string

Gene list inputs

Name	Type & Properties	Description
--s_genes	string multiple	List of gene symbols for scoring s phase genes.
--s_genes_file	file	Path to a .txt file containing the gene list of s phase genes to be scored. The gene list file should be formatted as a single column with gene symbols.
--g2m_genes	string multiple	List of gene symbols for scoring g2m phase genes.
--g2m_genes_file	file	Path to a .txt file containing the gene list of g2m phase genes 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.

Name

Type & Properties

--s_genes

string

multiple

--s_genes_file

file

--g2m_genes

string

multiple

--g2m_genes_file

file

--gene_pool

string

multiple

--gene_pool_file

file

Outputs

Name	Type & Properties	Description
--output	file required output	Output h5mu file
--output_compression	string	The compression format to be used on the output h5mu object.
--obs_phase	string	The name of the column in the obs attribute of the adata object that will store the cell cycle phase annotation.
--obs_s_score	string	The name of the column in the obs attribute of the adata object that will store the s phase score.
--obs_g2m_score	string	The name of the column in the obs attribute of the adata object that will store the g2m phase score.

Name

Type & Properties

--output

file

required

output

--output_compression

string

--obs_phase

string

--obs_s_score

string

--obs_g2m_score

string

Arguments

Name	Type & Properties	Description
--n_bins	integer	Number of expression level bins for sampling.
--random_state	integer	The random seed for sampling.
--allow_missing_genes	boolean	If true, missing genes in the gene list will be ignored.

Name

Type & Properties

--n_bins

integer

--random_state

integer

--allow_missing_genes

boolean

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_phase: [ "phase" ]  
obs_s_score: [ "S_score" ]  
obs_g2m_score: [ "G2M_score" ]  
n_bins: [ 25 ]  
random_state: [ 0 ]  
allow_missing_genes: [ false ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision 1.0.3 \  
  -main-script target/nextflow/feature_annotation/score_genes_cell_cycle_scanpy/main.nf \  
  -params-file params.yaml

feature_annotation/score_genes_cell_cycle_scanpy

Inputs

Gene list inputs

Outputs

Arguments

Run this component

Relationships

Used by

Uses