cirrocumulus


Namecirrocumulus JSON
Version 1.1.56 PyPI version JSON
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SummaryBring your single-cell data to life
upload_time2023-08-25 16:15:15
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requires_python>=3.9
licenseBSD 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.
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            Cirrocumulus
----------------

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

* Visualize datasets in h5ad_, `10x h5`_, Xenium_, loom_, Seurat_, TileDB_, or zarr_ formats
* View MERFISH_ or other spatial transcriptomics data overlaid on an image
* Easily deploy on a laptop, on-premise server, cloud VM, or Google App Engine
* 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 (`example ontology`_)
* 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
* 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


.. image:: images/play3d.gif

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/pbmc3k.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/
.. _TileDB: https://tiledb.com/
.. _zarr: https://zarr.readthedocs.io/
.. _example ontology: http://www.obofoundry.org/ontology/cl.html
.. _10x h5: https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/advanced/h5_matrices
.. _MERFISH: https://www.biorxiv.org/content/10.1101/2023.03.06.531121v1
.. _Xenium: https://www.10xgenomics.com/support/in-situ-gene-expression/documentation/steps/onboard-analysis/at-a-glance-xenium-output-files

            

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