Malva

Welcome to the Malva documentation.

Malva is a web application for searching single-cell and spatial transcriptomics data. You can search tens of thousands of single-cell samples by sequence expression and by metadata, then explore, compare, analyse, and share the results in your browser.

The paper

Read the Malva publication in Nature:

Read the Malva paper

What you can do

• Use the Expression Explorer to search for genes and sequences, inspect which cell types and samples express them, and filter by disease, organ, or study.
• Use the Coverage Explorer to inspect read coverage across a genomic region or a pasted DNA sequence in a zoomable, track-based browser.
• Use the Analysis workspace to save any set of cells as a group, compare groups with marker-gene and differential-expression analyses, and run GO enrichment.
• Use Sharing and history to share any search, result, or analysis with a link and to revisit everything you have done from your job history.

What you need to get started

1. Sign in with your ORCID account or a personal API token.
2. Run a search in the Expression Explorer. It accepts gene names, FASTA sequences, and natural-language queries such as "T cells in lung".
3. Browse the results in a live table, and open the coverage and analysis views as you go.

Live queries

The landing page offers Try a live query, which opens the Expression Explorer, and Inspect coverage, which opens the Coverage Explorer. You can use both without any setup.

First steps

• Getting started
• Expression Explorer tutorial
• Coverage Explorer tutorial

Documentation versions

Each release of Malva has a matching version of this documentation. Use the version selector at the top of this page to switch between released versions. The current version is shown in the footer of the web interface.

Is this documentation up to date?

Malva is under active development at the Rajewsky Lab, Max Delbrück Center, Berlin. If you find an error or a missing feature, open an issue on GitHub.