Software

velocyto

A package for the analysis of expression dynamics in single cell RNA seq data. For more information go to the velocyto homepage

cytograph

A tool for building analysis pipeline for big single cell RNA sequencing projects

loompy

Core implementation the standard format to store and work with single cell expression data. For more information go to the loompy homepage

nbregression

Negative binomial generalized linear model for single cell expression data

cmdstan-py

An alternative, lightweight, python interface to the Bayesian Modeling language Stan.

BackSPIN

Reference implementation of the clustering algorithm described in Zeisel et al. 2015

ceftools

An older file format designed to store smaller single-cell RNA seq datasets