Welcome to loompy!

loompy is a python library for working with the .loom file format.

.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. We use loom files to store single-cell gene expression data: the main matrix contains the actual expression values (one column per cell, one row per gene); row and column annotations contain metadata for genes and cells, such as Name, Chromosome, Position (for genes), and Strain, Sex, Age (for cells). Graph objects are used to store nearest-neighbor graphs used for graph-based clustering.

An illustration of the structure of the Loom format

Loom files (.loom) are created in the HDF5 file format, which supports an internal collection of numerical multidimensional datasets. HDF5 is supported by many computer languages, including Java, MATLAB, Mathematica, Python, R, and Julia. .loom files are accessible from any language that supports HDF5.