Installation

Manual installation

PROSSTT was developed and tested in Python 3.5 and 3.6. For an optimal experience, we suggest Python 3.6. In order to run PROSSTT, the following Python libraries have to be installed:

• scipy (tested: 1.0.0)
• numpy (tested: 1.14)
• pandas (tested: 0.22.0)
• newick (tested: 0.8.0)

In order to reproduce the example notebooks and produce plots with generate_simN.py the following libraries are additionally required:

• matplotlib (tested: 2.0.0, 2.1.2)
• jupyter (tested: 1.0.0)
• scanpy (tested: 0.4.2+9.ged7130f)

After installing all libraries:

• download a PROSSTT release or clone the git repository.
• (optional) unpack the archive
• cd prosstt/directory/
• pip install .

Install via Bioconda

(work in progress)