Welcome to the Phenonaut documentation!
Phenonaut is a framework for applying workflows to multi-omics data. Originally targeting high-content imaging and the exploration of phenotypic space, with different visualisations and metrics, Phenonaut allows now operates in a data agnostic manner, allowing users to describe their data (potentially multi-view/multi-omics) and apply a series of generic or specialised data-centric transforms and measures.
Phenonaut operates in 2 modes:
As a Python package, importable and callable within custom scripts.
Operating on a workflow defined in either YAML, or JSON, allowing integration of complex chains of Phenonaut instructions to be integrated into existing workflows and pipelines. When built as a package and installed, workflows can be executed with:
`python -m phenonaut workflow.yml`.
User guide
Alongside the API documentation a crash-course userguide is available here: User guide.
A breakdown and guide to workflow mode and commands can be found here: Workflow mode.
Contents:
- API documentation
- Subpackages
- phenonaut.data package
- phenonaut.integration package
- phenonaut.metrics package
- phenonaut.output package
- phenonaut.packaged_datasets package
- Submodules
- phenonaut.packaged_datasets.base module
- phenonaut.packaged_datasets.breast_cancer module
- phenonaut.packaged_datasets.cmap module
- phenonaut.packaged_datasets.iris module
- phenonaut.packaged_datasets.lincs module
- phenonaut.packaged_datasets.metadata_moa module
- phenonaut.packaged_datasets.tcga module
- Module contents
- phenonaut.predict package
- phenonaut.transforms package
- Submodules
- phenonaut.errors module
- phenonaut.phenonaut module
PhenonautPhenonaut.add_well_id()Phenonaut.aggregate_dataset()Phenonaut.append()Phenonaut.clone_dataset()Phenonaut.combine_datasets()Phenonaut.dataPhenonaut.describe()Phenonaut.dfPhenonaut.dsPhenonaut.filter_datasets_on_identifiers()Phenonaut.get_dataset_combinations()Phenonaut.get_dataset_index_from_name()Phenonaut.get_dataset_names()Phenonaut.get_df_features_perturbation_column()Phenonaut.get_hash_dictionary()Phenonaut.groupby_datasets()Phenonaut.keys()Phenonaut.load()Phenonaut.load_dataset()Phenonaut.merge_datasets()Phenonaut.new_dataset_from_query()Phenonaut.revert()Phenonaut.save()Phenonaut.shrink()Phenonaut.subtract_median_perturbation()
load()match_perturbation_columns()
- phenonaut.utils module
- phenonaut.workflow module
WorkflowWorkflow.VIF_filter_features()Workflow.add_well_id()Workflow.cityblock_distance()Workflow.copy_column()Workflow.euclidean_distance()Workflow.filter_columns()Workflow.filter_correlated_and_VIF_features()Workflow.filter_correlated_features()Workflow.filter_rows()Workflow.if_blank_also_blank()Workflow.load()Workflow.mahalanobis_distance()Workflow.manhattan_distance()Workflow.pca()Workflow.rename_column()Workflow.rename_columns()Workflow.run_workflow()Workflow.scalar_projection()Workflow.scatter()Workflow.set_perturbation_column()Workflow.tsne()Workflow.umap()Workflow.write_csv()Workflow.write_multiple_csvs()
predict()
- Module contents
PhenonautPhenonaut.add_well_id()Phenonaut.aggregate_dataset()Phenonaut.append()Phenonaut.clone_dataset()Phenonaut.combine_datasets()Phenonaut.dataPhenonaut.describe()Phenonaut.dfPhenonaut.dsPhenonaut.filter_datasets_on_identifiers()Phenonaut.get_dataset_combinations()Phenonaut.get_dataset_index_from_name()Phenonaut.get_dataset_names()Phenonaut.get_df_features_perturbation_column()Phenonaut.get_hash_dictionary()Phenonaut.groupby_datasets()Phenonaut.keys()Phenonaut.load()Phenonaut.load_dataset()Phenonaut.merge_datasets()Phenonaut.new_dataset_from_query()Phenonaut.revert()Phenonaut.save()Phenonaut.shrink()Phenonaut.subtract_median_perturbation()
PlatemapQuerierdataset_intersection()load()match_perturbation_columns()
- Subpackages
- User guide
- Publication examples
- Workflow mode