PfizerRD / cirrocumulus

Bring your single-cell data to life

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