Malva Client

Python client for the Malva genomic search platform. Search genes, sequences, and natural language queries across >7,000 single-cell and spatial transcriptomics samples.

For full documentation, visit malva-client.readthedocs.io.

Installation

pip install malva-client

For single-cell analysis workflows:

pip install malva-client scanpy

Authentication

Generate an API token at malva.bio (login with ORCID, then go to Profile > Generate API Token), then configure the client:

malva_client config --server https://malva.mdc-berlin.de --token YOUR_API_TOKEN

Quick Start (CLI)

malva_client search "CD3D" --output results.csv
malva_client search "ATCGATCGATCGATCGATCGATCG" --format json
malva_client search "CD4 T cells in brain tissue"

Quick Start (Python)

from malva_client import MalvaClient

client = MalvaClient("https://malva.mdc-berlin.de", "YOUR_API_TOKEN")

# Search for genes, sequences, or natural language queries
results = client.search("CD3D")
print(results)

# Search for sequences
results = client.search("ATCGATCGATCGCCACATGGACTTGAC")

# Natural language queries
results = client.search("cells expressing markers of neurodegeneration")

Working with Results

# Enrich results with metadata
results.enrich_with_metadata()
fig = results.plot_expression_summary("cell_type")

# Filter and aggregate
filtered = results.filter_by(disease='normal', organ='brain')

See the tutorials for coverage analysis, dataset discovery, cell-level searches, and more.

Indexing Your Own Data

For local indexing and quantification, see Malva Tools (malva CLI).

Citation

If you use Malva in your research, please cite:

[TBA]

License

The Clear BSD License - Copyright (c) 2025-2026 Malva