Welcome to loompy!

loompy is a python library to agilely work with the .loom file format.

.loom is an efficient file format for very large omics datasets, consisting of a main matrix, optional additional layers, and a variable number of row and column annotations. 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).

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.