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
Position (for genes), and
Age (for cells). Graph objects are used to store nearest-neighbor
graphs used for graph-based clustering.
Loom files (
.loom) are created in the
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.
files are accessible from any language that supports HDF5.
LoomR implements loom for R from Rahul Satija’s lab
scanpy from Fabian Theis lab now reads and writes loom files directly.
- API Walkthrough
- Complete API Reference