Metadata-Version: 2.1
Name: cirrocumulus
Version: 1.1.22.post3
Summary: Single-cell visualization application
Home-page: https://github.com/klarman-cell-observatory/cirrocumulus
Author: Joshua Gould
Author-email: jgould@broadinstitute.org
License: UNKNOWN
Description: 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
        * 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/
        
        
Keywords: single cell/nucleus genomics visualization
Platform: UNKNOWN
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Natural Language :: English
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Visualization
Requires-Python: >=3.6
Description-Content-Type: text/x-rst
Provides-Extra: test
