Cellenics is an open-source platform aimed at empowering research biologists to analyze their own single-cell and spatial RNA sequencing datasets. In collaboration with the HMS Single Cell Core, the Harvard Chan Bioinformatics Core, input from the Biopolymers Facility and the Center for Computational Biomedicine, we developed a user-facing application for project management as well as data processing, quality control, and visualization (Fig. 1). These modules enable in-depth data exploration through differential expression and pathway analyses as well as the generation of fully customizable plots for publication.
Cellenics consists of multiple repositories - the codebase of the platform itself, as well as repositories that define the AWS infrastructure and provide various utilities.
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- pipeline - Bioinformatics repository for the Data Processing module.
- worker - Bioinformatics repository for running analyses on processed datasets.
- ui - User interface for the platform built with React/Redux.
- api - A nodejs service that sits in between the UI and the Cellenics backends (pipeline, worker).
- iac - AWS Infrastructure as Code and GitOps repository.
Figure 1: Cellenics Platform. Cellenics is an open-source, cloud-based platform developed in the Department of Biomedical Informatics. A. Current Cellenics Modules developed in Phases 1 & 2. B. Data Processing module. C. Data Exploration module. D. Differential expression tool within the Data Exploration module. E. Plots and Tables module.
Need help with your analysis? Here are some brief tutorials:
There is also a more in-depth recorded workshop (~2 hours).
For information about the Cellenics project's principles and practices, licensing, and a list of maintainers, please see the governance repo.
