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
3 maintainers
Metadata
3 maintainers
Release files for cirrocumulus 1.1.22.post10
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| cirrocumulus-1.1.22.post10.tar.gz | 3.2 MB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| cirrocumulus-1.1.22.post10-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 5.9 MB
Release files / cirrocumulus-1.1.22.post10.tar.gz
| Download URL | cirrocumulus-1.1.22.post10.tar.gz |
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| Size | 3.2 MB |
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Release files / cirrocumulus-1.1.22.post10-py3-none-any.whl
| Download URL | cirrocumulus-1.1.22.post10-py3-none-any.whl |
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| Size | 2.6 MB |
| Tags | Python 3 |
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