Scarf¶
Scarf is a Python package that performs memory-efficient analysis of single-cell genomics data.
Analyze atlas scale datasets on your laptop (tested with up to 4 million cells)
Perform analysis of scATAC-Seq data (datasets with up to 700K cells with 1 million peaks tested) under 10 GB RAM
Make parallel implementations of UMAP and tSNE (SG-tSNE) for quick cell embedding
Perform hierarchical clustering that gives interpretable cluster relationships
Sub-sample highly representative cells using state-of-the-art TopACeDo method
Perform quick and accurate projections of cells from one dataset onto another or integrate multiple datasets.
- Installation
- Vignettes
- Scarf’s basic workflow for scRNA-Seq
- Workflow for scATAC-Seq data
- Handling datasets with multiple modalities
- Cell subsampling using TopACeDo
- Projection of cells across datasets
- Merging datasets and partial training
- Understanding how data is organized in Scarf
- Data import and export in Scarf
- Running notebooks live on Google Colab
- FAQs
- API
- License
- Index