Single cell RNA seq data analysis

Question

[asharmatelome]

Hi, I am a wet-lab researcher with minimum exposure to computational biology. But I am very keen to learn next-gen data analysis. Recently, I have done single cell RNA-seq and though our computational collaborator is helping with data analysis. I myself want to explore this data, I wonder if there are some web-based pipelines to do single cell data analysis? Thanks in advance! Ankur

[Madelaine Gogol]

No.

(Sorry. For a more helpful and less grumpy answer, there are a lot of web based things you can do once you have, say, a list of genes or something). But single cell data is sort of notoriously complex, with lots of missing and low values. So it's not yet the type of thing that is amenable to plugging into a web form.

Answer 1

[Kamil]

If you can use R, then you can analyze single-cell RNA-seq data. Check out these packages and their associated tutorials. My recommendation is that you analyze the example data files first to get a sense of how things work, and then try your own data later.

• SCDE https://github.com/hms-dbmi/scde
• Seurat https://github.com/satijalab/seurat