decima.cli package¶
Submodules¶
decima.cli.attributions module¶
Attributions CLI.
This module contains the CLI for the attributions module performing attribution analysis, seqlet calling, and motif discovery.
decima attributions is the main command for performing attribution analysis, seqlet calling, and motif discovery.
It includes subcommands for: - Predicting attributions for a given gene or sequence. attributions-predict - Seqlet calling on the attributions. attributions - Motif discovery on the attributions. attributions-recursive-seqlet-calling - Plotting the attributions. attributions-plot
Examples
>>> decima attributions -o output_prefix -t tasks -o off_tasks -m model -m metadata -m method -m transform -m batch_size -m genes -m top_n_markers -m disable_bigwig -m disable_correct_grad_bigwig -m device -m genome -m num_workers
...
decima.cli.callback module¶
decima.cli.download module¶
Download CLI.
This module contains the CLI for downloading the required data and model weights.
decima download is the main command for downloading the required data and model weights.
It includes subcommands for: - Caching the required data and model weights. cache
decima.cli.finetune module¶
Finetune the Decima model.
This module contains the CLI for finetuning the Decima model.
decima finetune is the main command for finetuning the Decima model.
It includes subcommands for: - Finetuning the Decima model. finetune
decima.cli.modisco module¶
Modisco CLI.
This module contains the CLI for the modisco module performing motif discovery and analysis.
decima modisco is the main command for performing motif discovery and analysis.
It includes subcommands for: - Computing attributions for a given gene or sequence. modisco-attributions - Discovering motifs on the attributions. modisco-patterns - Reporting the motifs. modisco-reports - Extracting the seqlets from the modisco results. modisco-seqlet-bed
Examples
>>> decima modisco -o output_prefix --tasks "cell_type == 'classical monocyte'" --genes SPI1,CD68
>>> decima modisco -o output_prefix --tasks "cell_type == 'B cell'" --device 0 --genome hg38
>>> decima modisco -o output_prefix --genes SPI1 --method saliency --batch-size 2
decima.cli.predict_genes module¶
Predict Genes CLI.
This module contains the CLI for predicting the gene expression of a given gene or sequence.
decima predict-genes is the command for predicting the gene expression of a given gene or sequence.
decima.cli.query_cell module¶
Query Cell CLI.
This module contains the CLI for querying the cell metadata.
decima query-cell is the command for querying the cell metadata.
Examples
>>> decima query-cell 'cell_type == "classical monocyte"'
...
>>> decima query-cell 'cell_type == "classical monocyte" and disease == "healthy" and tissue == "blood"'
...
>>> decima query-cell 'cell_type.str.contains("monocyte") and disease == "healthy"'
...
decima.cli.vep module¶
Variant Effect Prediction CLI.
This module contains the CLI for predicting the variant effect.
decima vep is the main command for predicting the variant effect.
It includes subcommands for: - Predicting the variant effect. vep - Ensembling the variant effect predictions. vep-ensemble
Examples
>>> decima vep -v "data/sample.vcf" -o "vep_results.parquet"
...
>>> decima vep -v "data/sample.vcf" -o "vep_results.parquet" --tasks "cell_type == 'classical monocyte'" # only predict for classical monocytes
...
>>> decima vep -v "data/sample.vcf" -o "vep_results.parquet" --device 0 # use device gpu device 0
...
decima.cli.vep_attribution module¶
Interpretation of Variant Effect Prediction with Attribution Analysis CLI.