Flotilla: An Open-Source Toolkit for Single-Cell RNA-Seq Data Analysis in Multiple Organisms

We present flotilla (https://github.com/YeoLab/flotilla) as an open source, community-driven software package written in Python that enables biologists with rudimentary knowledge of statistical methods and programming to analyze and visualize hundreds of RNA-seq datasets. Our package includes interactive functions for common and important tasks in computational analyses of biological datasets such as dimensionality reduction, covariance analysis, classification, regression and outlier detection. Since the field is constantly evolving new methods for quantification, flotilla flexibly adapts to various different upstream workflows that quantify gene expression or splicing. As a case study, we will present features from our analysis of RNA-seq data from hundreds of individual cells isolated during in vitro differentiation of human induced pluripotent stem cells towards the motor neuron lineage using flotilla. With these data, we show the utility of flotillain quantifying the heterogeneity of gene expression and mRNA splicing at the single cell level. We can extract gene regulatory networks that represent novel factors that influence neuronal maturity.

*Michael T Lovci and Olga B Botvinnik contributed equally to this work. 

This work is funded by grants from NIH and CIRM to G.W.Y. and from the NumFOCUS foundation to O.B.B.