Search the raw sequence space of single-cell atlases

Malva enables ultrafast, reference-free interrogation of petabyte-scale single-cell and spatial transcriptomics data. Search for any sequence, mutation, splice junction, or transcript directly — no downloads, no preprocessing.

Auto-updated — crawling HCA, GEO & more
Sequence-level — beyond gene matrices
Instant — milliseconds across 50M+ cells
0 M cells
0 experiments
0 organisms
0 faster

One search across all public single-cell data

Malva continuously crawls and indexes single-cell & spatial transcriptomics from public repositories. Search by sequence to find what gene expression matrices miss.

Auto-Updated

Continuously crawling HCA, GEO, and other public repositories. New datasets indexed automatically as they're published.

Sequence-Level

Go beyond gene counts. Search for any k-mer, splice junction, mutation, pathogen sequence, or transcript variant.

Reference-Free

Species-agnostic search without requiring genome alignments. Discover sequences that references miss.

Find the exact cells you need

Query any sequence, gene, or concept — Malva instantly returns matching cells from millions indexed across public atlases.

1

Your query

Sequence, gene, or natural language

2

Malva Index

51M+ cells from thousands of studies

3

Matching cells

Ready to explore and analyze

🧬

Sequence

Paste any DNA/RNA

ATGCTAGC...
🔬

Gene

Enter gene symbols

CD28, FOXP3
💬

Natural Language

Just describe it

"T cells in lung"
01
Query

Search any sequence directly

Standard pipelines discard raw sequences, keeping only gene counts. Malva indexes the actual sequence content, letting you search for k-mers, mutations, splice variants, or pathogen sequences that gene matrices miss entirely.

No reference genome required
Find mutations & variants
Detect pathogen sequences
Query Input
ATGCTAGCTAGCTAGCTAGCATGC
02
Index

Search millions of cells in milliseconds

The Malva Index currently comprises ~60 million cells from thousands of experiments in health and disease. Our indexing technology enables millisecond queries across what would otherwise require downloading and processing terabytes of raw data.

Sub-second query response
Continuously growing index
No data download required
Malva Index
0.00ms
Query Time
03
Results

Cell-level resolution

Get exact matches at single-cell resolution with full metadata. See which cells contain your sequence, their tissue of origin, disease state, and source study — all linked back to the original data.

Complete cell metadata
Linked to source studies
Export for downstream analysis
Search Results
🧬
T Cells (CD4+)
Lung tissue • 12 studies
45,231
🔬
B Cells
Blood • 8 studies
23,847
📊
Macrophages
Multiple tissues • 15 studies
12,156

Transform atlases from static tables into searchable sequence resources

Free for academic and non-profit research. Start searching across millions of cells in seconds.

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