Reference

Covim.

Import the package:

import lnschema_covim as cv

ORMs:

Biosample(*args, **kwargs)	Biosamples for the Covim consortium.
Infection(*args, **kwargs)	ICD-10 code of secondary infections.
Comorbidity(*args, **kwargs)	Comorbidity of the patient, in ICD-10 code.
Medication(*args, **kwargs)	ATC-code of the medication given (https://www.whocc.no/atc_ddd_index/).
Study(*args, **kwargs)	Covim studies.

Wrapper functions for ingestion:

inspect_markers(data[, curate_function, ...])	Inspect cell markers.
standardize_markers(adata[, add_new, var_key])	Standardize cell marker names.
ingest_markers(meta[, curate_function, ...])	Ingest data from the CovimBiosampleForm.
list_files_from_biosample_form(meta[, basedir])	Gets list of files from biosample form.
rename_featureset_members(artifacts, ...)	Renames members of FeatureSets of AnnData Artifacts.

Transfer functions:

transfer_artifact_to_immunohub(artifact, *)	Saves a local artifact to the remote schultzelab/covimdata instance.
transfer_biosample_to_immunohub(biosample)	Saves an existing biosample to the current instance.

Test datasets

datasets

Small example datasets.

Test datasets

types

Types.