scRNA-seq analysis with Cellenics®
In her article, Ziwen Cass Li describes her step-by-step scRNA-seq analysis with Cellenics®, an open source data analytics tool. She explores the question - what are the transcriptomic differences between the developing and adult mouse brains at the single-cell level?
"Having in-house bioinformaticians who can process and analyze your single-cell RNA sequencing data is a luxury that many research groups want but don't have. The alternative is either to queue for services provided by bioinformaticians embedded in other groups or outsource the tasks to specialized companies. The former often become bottlenecks of your research pipeline, and the latter can only be viable with sufficient funds. You might feel like running out of options, but don't worry, here comes Cellenics®. It is an open-source tool for secondary data analysis and visualization. The Biomage-hosted community instance of Cellenics® is free for academic users.”
“As a bioinformatician myself, I enjoy building my analysis pipelines for single-cell datasets. However, I don't think that programming skills should be standing between the researchers and their datasets. Our ultimate goal is to understand the scientific implication of the data and use that knowledge to push our research further and benefit more people. To this end, we need a tool that is easy to use and quick to generate results (plots, graphs, and differentially expressed gene lists), and Cellenics® is such a tool. Let me show you what Cellenics® can do for you and your datasets."
Dot plot of top differentially expressed genes that are upregulated in the developmental brain (grouped by Louvain clusters).
UMAP showing Louvain clusters after Data Processing.
"You can carry out complex analyses at different granularity levels and ultimately tell a good story based on your research and data analysis. With the flexibility and functionality provided by Cellenics®, you are ready to tell that story to your colleagues, your students, the reviewers of your papers and grants, to everyone out there who is interested in your research.
So what are you waiting for?"
Read the full article on Cass Li's website:
https://www.ziwencassli.com/single-cell-genomics/scrna-seq-analysis-with-cellenics
Start your analysis now using the Biomage-hosted community instance of Cellenics® at https://scp.biomage.net/
Interested in mastering single cell RNA-seq data analysis? Biomage offers an in-depth online course to guide you through each step. Dive into our blog post to learn more: Unlock the Secrets of Single-Cell RNA-Seq Data Analysis with Our Comprehensive Course