countland includes a set of functions for applying a restricted linear algebra to the analysis of count-based data. This tool is specifically designed to analyze count matrices from single cell RNA sequencing assays. The tool implement several count-based approaches for standard steps in scRNA-seq analysis, including scoring genes and cells, comparing cells and clustering, calculating differential gene expression, and several methods for rank reduction. There are many opportunities for further optimization that may prove useful in the anlaysis of other data. We provide the source code freely available at https://github.com/shchurch/countland and encourage users and developers to fork the code for their own purposes.
Package upstream: https://github.com/shchurch/countland
I packaged this for easy installation using conda, but I am not affiliated with the project!
