Abstract
BackgroundSingle cell transcriptome sequencing has become an increasingly valuable technology for dissecting complex biology at a resolution impossible with bulk sequencing. However, the gap between the technical expertise required to effectively work with the resultant high dimensional data and the biological expertise required to interpret the results in their biological context remains incompletely addressed by the currently available tools.ResultsSingle Cell Explorer is a Python-based web server application we developed to enable computational and experimental scientists to iteratively and collaboratively annotate cell expression phenotypes within a user-friendly and visually appealing platform. These annotations can be modified and shared by multiple users to allow easy collaboration between computational scientists and experimental biologists. Data processing and analytic workflows can be integrated into the system using Jupyter notebooks. The application enables powerful yet accessible features such as the identification of differential gene expression patterns for user-defined cell populations and convenient annotation of cell types using marker genes or differential gene expression patterns. Users are able to produce plots without needing Python or R coding skills. As such, by making single cell RNA-seq data sharing and querying more user-friendly, the software promotes deeper understanding and innovation by research teams applying single cell transcriptomic approaches.ConclusionsSingle cell explorer is a freely-available single cell transcriptomic analysis tool that enables computational and experimental biologists to collaboratively explore, annotate, and share results in a flexible software environment and a centralized database server that supports data portal functionality.
Highlights
Single cell transcriptome sequencing has become an increasingly valuable technology for dissecting complex biology at a resolution impossible with bulk sequencing
We showed the case of using a Jupyter notebook to drive a 10X genomics based cell processing pipeline
For Jupyter notebook users, we provided scpipeline, which is a python script for a helper function that runs Cell Ranger and loads the result to MongoDB
Summary
Single Cell Explorer is a Python-based web server application we developed to enable computational and experimental scientists to iteratively and collaboratively annotate cell expression phenotypes within a user-friendly and visually appealing platform. These annotations can be modified and shared by multiple users to allow easy collaboration between computational scientists and experimental biologists. The application enables powerful yet accessible features such as the identification of differential gene expression patterns for user-defined cell populations and convenient annotation of cell types using marker genes or differential gene expression patterns. By making single cell RNA-seq data sharing and querying more user-friendly, the software promotes deeper understanding and innovation by research teams applying single cell transcriptomic approaches
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