Python implementation of the Loom file format -
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slinnarsson Merge pull request #73 from Riseley/patch-1
fix critical typo in docs
Latest commit 9611372 Sep 16, 2018

loompy 2

⭐ Loompy v2.0 was released Dec. 24, 2017! (what's new?)

.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. Loom also supports sparse graphs. 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).

Illustration of Loom format structure

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.

To get started, head over to the documentation!

Loom, loompy, and the loom-viewer are being developed by members of the Linnarsson Lab.