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.. loompy documentation master file, created by
sphinx-quickstart on Tue Oct 3 00:11:17 2017.
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
Loompy documentation
====================
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.
The Loom logo illustrates how all the parts fit together:
|
.. image:: Loom_components.png
:width: 976px
:height: 345px
:scale: 50 %
:align: center
|
Loom files (``.loom``) are created in the
`HDF5 <https://en.wikipedia.org/wiki/Hierarchical_Data_Format>`__ file
format, which supports an internal collection of numerical
multidimensional datasets. HDF5 is supported by many computer languages,
including `Python <http://h5py.org>`__,
`R <http://bioconductor.org/packages/release/bioc/html/rhdf5.html>`__,
`MATLAB <http://se.mathworks.com/help/matlab/low-level-functions.html>`__,
`Mathematica <https://reference.wolfram.com/language/ref/format/HDF5.html>`__,
`C <https://www.hdfgroup.org/HDF5/doc/index.html>`__,
`C++ <https://www.hdfgroup.org/HDF5/doc/cpplus_RM/>`__,
`Java <https://www.hdfgroup.org/products/java/>`__, and
`Ruby <https://rubygems.org/gems/hdf5/versions/0.3.5>`__.
.. toctree::
:hidden:
self
installation/index
semantics/index
kallisto/index
apiwalkthrough/index
cookbook/index
conventions/index
format/index
fullapi/index
|
