The shunPykeR's guide to single cell RNA-seq analysis

This is the first pre-release of the shunPykeR's guide to the single cell RNA-seq analysis pipeline. This pipeline represents a complete guide for the analysis of scRNA-seq datasets in a Jupyter notebook format. This guide has been simplified by hiding more complex code snipsets behind the scenes (within the shunpiker_modules.pyfile) allowing non computational scientists to perform a robust and thorough analysis of their scRNA-seq datasets with (relative) peace of mind. However, it can also be used by bioinformaticians that may want to adjust it and reuse it in their own way.

Within this guide we have brought together a combination of already established scRNA-seq analysis tools, that we have put together in a logical order to simplify running your analysis. The main code is in python but it is interpolated snippets of R code to take advantage both worlds when using scRNA-seq developed algorithms.