This release is a pre-release and may not be stable for production use.
Scarf
[!IMPORTANT] Scarf 1.0 is coming soon. Install the
release candidate with
uv pip install --prerelease allow "scarf[extra]". The current stable release on PyPI is0.32.3.
Scarf is a Python framework for analysing single-cell RNA, ATAC, protein, and multi-omic data, from a few thousand cells to tens of millions.
| Problem | How Scarf solves it | What you get |
|---|---|---|
| Your dataset is larger than RAM | Out-of-core algorithms, and neighbour search streams from cell-major and gene-major layouts, inside a memory budget you set | No subsampling, so rare populations survive, benchmarked to 10M cells |
| The data is stored remotely and requires downloading | Fetches only the chunks an operation touches, and writes results to a store you own | Start analysing immediately, with one authoritative copy |
| A single parameter change costs hours of computation | Each step is fingerprinted by its settings and inputs, so reuse is by content, not by layer name | Only what changed recomputes, and the old version stays for comparison |
| Sub-population analysis leaves scattered copies that nobody can trace back | Subsets are masks in one file, and every result carries the cells and parameters behind it | A year later, a result still explains itself |
Install
Python 3.12+.
uv venv --python 3.12
uv pip install --python .venv "scarf[extra]"
Detailed installation instructions here
Quick start
import scarf
ds = scarf.DataStore(
"s3://bucket/10M_cells.zarr", # also gs://, hf://, or a local path
)
ds.pipeline.run() # convenience: QC → HVGs → PCA → graph → UMAP → clustering → markers
ds.plots.embedding(
layout_key="RNA_UMAP",
color_by="RNA_clusters",
)
Read the scRNA-seq tutorial for a granular workflow, or remote stores for cloud setups.
Documentation
Read workflow vignettes and API references on Read The Docs 📖
AI-assisted and autonomous workflows should start with Analysis with AI agents.
Scarf's capabilities
| Area | Methods |
|---|---|
| Modalities | scRNA-seq, scATAC-seq, CITE-seq, matched multi-omics |
| Core workflow | Quality control, feature selection, normalization, PCA and LSI, KNN graph, UMAP, densMAP, t-SNE, Leiden, Paris, marker search |
| Integration | Harmony, partial PCA, shared and weighted nearest neighbours, integration metrics |
| Mapping | Symphony-style reference mapping, label transfer, projection diagnostics |
| Trajectory | Population Balance Analysis pseudotime, expression dynamics and modules, multi-sink fate probabilities |
| Also included | Cell-cycle scoring, gene-set activity, graph-diffusion imputation, doublet scores, HTO demultiplexing, TopACeDo downsampling, pseudobulk export |
Citation
Dhapola et al. Scarf enables a highly memory-efficient analysis of large-scale single-cell genomics data. Nature Communications 13, 4616 (2022).
Support
Scarf is open source software released under the BSD 3-Clause License and maintained by Nygen.
1 maintainer
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