Metadata-Version: 2.1
Name: cirrocumulus
Version: 1.1.33
Summary: Bring your single-cell data to life
Project-URL: Documentation, https://cirrocumulus.readthedocs.io/
Project-URL: Source, https://github.com/klarman-cell-observatory/cirrocumulus
Author-email: Joshua Gould <cirrocumulus@googlegroups.com>
License: BSD 3-Clause License
        
        Copyright (c) 2022, klarman-cell-observatory
        All rights reserved.
        
        Redistribution and use in source and binary forms, with or without
        modification, are permitted provided that the following conditions are met:
        
        1. Redistributions of source code must retain the above copyright notice, this
           list of conditions and the following disclaimer.
        
        2. Redistributions in binary form must reproduce the above copyright notice,
           this list of conditions and the following disclaimer in the documentation
           and/or other materials provided with the distribution.
        
        3. Neither the name of the copyright holder nor the names of its
           contributors may be used to endorse or promote products derived from
           this software without specific prior written permission.
        
        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: Implementation :: PyPy
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Visualization
Requires-Python: >=3.7
Requires-Dist: anndata
Requires-Dist: cachecontrol
Requires-Dist: flask
Requires-Dist: flask-compress
Requires-Dist: fsspec
Requires-Dist: gunicorn
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: pyarrow
Requires-Dist: pymongo
Requires-Dist: scipy
Requires-Dist: zarr
Provides-Extra: dev
Requires-Dist: black; extra == 'dev'
Requires-Dist: isort; extra == 'dev'
Requires-Dist: pre-commit; extra == 'dev'
Provides-Extra: test
Requires-Dist: mongomock; extra == 'test'
Requires-Dist: pytest; extra == 'test'
Requires-Dist: scanpy; extra == 'test'
Description-Content-Type: text/x-rst

Cirrocumulus
----------------

Cirrocumulus is an interactive visualization tool for large-scale single-cell genomics data, with the following features:

* Easily deploy on a laptop, on-premise server, cloud VM, or Google App Engine
* View spatial transcriptomics data overlaid on an image
* Share the current visualization state in a URL
* Share datasets securely with collaborators
* Create dotplots, heatmaps, and violin plots to explore relationships between categorical variables and expression
* Generate composition plots to inspect cluster makeup
* Explore complete differential expression results generated by `Scanpy`_ or `Pegasus`_/`Cumulus`_
* Interactively create and share “AND” or “OR” filters
* Collaboratively annotate cell types in real time (optionally using a controlled vocabulary)
* Quickly load multiple features from predefined lists (`see example`_)
* Explore multiple features and embeddings simultaneously
* Fast interactive exploration of 2 and 3-d embeddings of millions of cells, including zoom, pan, rotate (3-d), and lasso tools
* Save publication quality images
* Visualize datasets in h5ad_, loom_, Seurat_, TileDB_, zarr_, or `STAR-Fusion`_  formats
* Highly customizable - for example, set the color map, point size, or whether to use fog for 3-d embeddings to fade distant points


Quick Start
-------------

Install the package::

    pip install cirrocumulus

Launch cirrocumulus via the command line::

    cirro launch <path_to_dataset>

- Launch accepts more than one dataset to enable quick dataset switching or to combine modalities (e.g gene fusions and expression) stored in separate files.

Example Data
^^^^^^^^^^^^^

- Download `3k PBMCs from a healthy donor data`_ and launch::

    cirro launch pbmc3k.h5ad --markers markers.json


- Download `human lymph node spatial data`_ and launch::

    cirro launch V1_Human_Lymph_Node/V1_Human_Lymph_Node.h5ad --spatial V1_Human_Lymph_Node/spatial


Complete documentation available at https://cirrocumulus.readthedocs.io


.. _3k PBMCs from a healthy donor data: https://github.com/klarman-cell-observatory/cirrocumulus/raw/master/docs/example_data.zip
.. _human lymph node spatial data: https://github.com/klarman-cell-observatory/cirrocumulus/raw/master/docs/V1_Human_Lymph_Node.zip
.. _h5ad: https://anndata.readthedocs.io/
.. _loom: https://linnarssonlab.org/loompy/format/
.. _STAR-Fusion: https://github.com/STAR-Fusion/STAR-Fusion/wiki
.. _Seurat: https://satijalab.org/seurat/
.. _see example: https://github.com/klarman-cell-observatory/cirrocumulus/raw/master/docs/markers.json
.. _Pegasus: http://pegasus.readthedocs.io/
.. _Cumulus: https://cumulus.readthedocs.io/en/stable/cumulus.html
.. _Scanpy: https://scanpy.readthedocs.io/
.. _zarr: https://zarr.readthedocs.io/
.. _TileDB: https://tiledb.com/
