Welcome to Loom, loompy, and the loom viewer!
Loom is a file format designed to store and work with single-cell RNA-seq data. Loom can also be used more generally for any type of omics data that is naturally represented as a matrix.
- Single file that can be moved around
- Keep metadata with expression data
- Data, clustering, layout, annotation stored together
- Efficient random access
- Automatic, on-the-fly compression
- Any programming language
- First-class Python API
- Out-of-memory data processing
- Open source, BSD license
To get started, head over to the docs
Source code is available at GitHub for loompy and loom-viewer.
LoomR from Rahul Satija’s lab implements loom for R
scanpy from Fabian Theis lab reads and writes loom files directly.