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.
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 |
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. |
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. |
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 v4.0.1 \
-main-script target/nextflow/feature_annotation/score_genes_scanpy/main.nf \
-params-file params.yaml Relationships
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Current component
feature_annotation/score_genes_scanpyopenpipeline v4.0.1
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