lilab-bcb / cirrocumulus

Bring your single-cell data to life
https://cirrocumulus.readthedocs.io/
BSD 3-Clause "New" or "Revised" License
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10x anndata bioinformatics data-visualization scanpy scrna-seq seurat single-cell smartseq2 spatial transcriptomics visualization webgl

Cirrocumulus

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

Quick Start

Install the package::

pip install cirrocumulus

Launch cirrocumulus via the command line::

cirro launch <path_to_dataset>

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

.. 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