camaralab/sctda

An object oriented python library for topological data analysis of high-throughput single-cell RNA-seq data

scTDA

scTDA is an object oriented python library for topological data analysis of high-throughput single-cell RNA-seq data. It includes tools for the preprocessing, analysis, and exploration of single-cell RNA-seq data based on topological representations.

Installation

To install scTDA run:

pip install scTDA

Alternatively, to install the most updated version you can download the source code and run:

python setup.py install

For optimal visualization results it is strongly recommended to have Graphviz tools and PyGraphviz installed.

Docker

A Docker container with a fully configured jupyter notebook environment and scTDA can be obtained running:

docker pull pcamara/sctda

To start the image use:

docker run -it -v /path/to/your/working/directory:/home/jovyan/work --rm -p 8888:8888 pcamara/sctda

where /path/to/your/working/directory is the folder containing the data you want to analyze. In some systems it may be required replacing /home/jovyan/work with //home/jovyan/work in the above command.

Using scTDA

scTDA can be imported using the command:

import scTDA

A tutorial illustrating the basic scTDA workflow can be found in doc/scTDA Tutorial.html. The source notebook and data files for the tutorial can be downloaded here. For optimal visualization when working with notebooks, we recommend using %matplotlib notebook.

More details on the scTDA algorithm can be found in:

Rizvi, A. H.*, Camara, P. G.*, Kandror, E. K., Roberts, T. J., Scheiren, I., Maniatis, T., and Rabadan, R., "Single-Cell Topological RNA-Seq Analysis Reveals Insights Into Cellular Differentiation and Development", Nat. Biotechnol. (2017) 35: 551-560. [* These authors contributed equally to this work.]