Loom is an efficient file format for very large omics datasets, consisting of a main matrix, optional additional layers, a variable number of row and column annotations, and sparse graph objects. Loom files are portable, self-contained and ensure that metadata travels with the data. Under the hood, Loom files are HDF5 and can be opened from many programming languages, including Python, R, C, C++, Java, MATLAB, Mathematica, and Julia. The Loom file format is natively supported by popular scRNA-seq packages including Scanpy, Seurat, SCope and scVI. (LoomPy, RRID:SCR_016666)

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S. Linnarson Lab (, Karolinska Institute