About Malva

Malva is a genomic search platform that provides access to harmonized single-cell and spatial transcriptomics data. The platform enables researchers to search across thousands of samples for gene expression patterns, sequences, and biological signatures.

Key Features

Large-Scale Data

Access to over 7,000 single-cell samples across diverse tissues, conditions, and species — all queryable through a single API.

Real-time Search

Instantaneous results powered by a k-mer index. No reprocessing of raw data — just query and get answers.

Multiple Query Types

Gene symbols, natural language queries, DNA sequences, and batch search. From single genes to genome-scale probes.

Harmonized Metadata

Standardized metadata across studies for consistent cross-dataset analysis — cell types, organs, diseases, and more.

Use Cases

Expression & Biomarkers
🧬

Gene expression analysis, biomarker discovery, and cell-type characterization across studies.

Sequence Events
🔬

Circular RNA detection, splice-junction discovery, SNV screening, and fusion transcript identification.

Pathogen & Rare Events
🦠

Viral/bacterial transcript quantification and low-frequency sequence detection missed in individual studies.

Data Sources

Malva integrates data from:

  • Human Cell Atlas datasets

  • Published single-cell studies

  • Spatial transcriptomics experiments

  • Disease-focused research cohorts

All data is processed through standardized pipelines with consistent quality control and metadata annotation.

Indexing Your Own Data

For indexing and quantifying your own data locally, use Malva Tools (the malva command-line suite), not the Malva Client. Malva Tools provides local indexing, quantification, and analysis capabilities:

# Index a reference transcriptome
malva index --fasta transcriptome.fa --output my_index

# Quantify single-cell data against the index
malva quant --index my_index --reads sample_R2.fastq.gz --output counts.h5ad

Malva Tools documentation: malva.readthedocs.io

Malva Tools source code: github.com/malva-bio/malva

Contact

For questions or support, contact the Malva team at hello@malva.bio.

More information available at malva.bio.