Cirrocumulus is an interactive visualization tool for large-scale single-cell genomics data, with the following features:
10x h5
, Xenium, loom, Seurat, TileDB, or zarr_ formatsScanpy
or Pegasus
/Cumulus
_example ontology
_)see example
_)Install the package::
pip install cirrocumulus
Launch cirrocumulus via the command line::
cirro launch <path_to_dataset>
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