cellula

This is the companion website to the cellula package.

cellula is a simple R-based pipeline for single cell RNA-seq processing with a number of methods for integration and identity assignment.

cellula follows the practices outlined in the OSCA book [1], with some additional options for integration/batch effect correction methods, signature scoring, and downsampling.

As a one-stop solution, this package tends to make choices for the users, with the caveat that these choices follow either defaults or sensible implementations. However, this means that a certain degree of freedom is removed from the end user. This assumes that users who desire total control on the process (or granular specification of parameters) do not need cellula and would be more comfortable setting up their own analysis pipelines.

cellula exists to automate and share routine analyses the way I usually do them, and offer “quick and dirty” access for exploratory data analysis.

cellula is very much under active development, and any feedback and contribution are welcome through the Issues page.

Where did the name “papplain” come from? it’s an inside joke with some friends and ex colleagues.

Why did you change it to “cellula”? one day I’d like to share this tool and I need a name that is not too dumb.