Cirrocumulus

Joshua Gould, Yiming Yang, Bo Li
2019-10-30
Code

Cirrocumulus is an interactive web application for exploring single cell datasets. It can be hosted on Google App Engine application for collaborative use or can be run in standalone mode on a personal computer. Cirrocumulus consists of a client-side component implemented in JavaScript and a server component implemented in Python. The client uses React to manage state and WebGL to visualize variables on a 2D or 3D embedding in a performant manner. The server component consists of functions to manage datasets, slice variables from a dataset stored as a folder of JSON and PARQUET files, and can optionally generate statistical summaries on an n-dimensional grid, thus enabling plotting of millions of cells. Cumulus has options to generate the Cirrocumulus input folder automatically for users. In the standalone mode, Cirrocumulus can additionally support datasets in AnnData or Zarr formats.

Click here to read Cirrocumulus documentation

Cirrocumulus is released on PyPI as a Python package.

Publications:

Yiming Yang
Yiming Yang
Computational Scientist

Yiming Yang is a computational scientist in Li Lab.

Bo Li
Bo Li
Assistant Professor of Medicine and Director of Bioinformatics and Computational Biology Program

Dr. Li’s research focuses on developing reliable computational tools to empower novel analyses of various Next-Generation Sequencing (NGS) data, and in particular, single-cell genomics data.