congas

Copy number genotyping from scRNA sequencing

A set of Pyro models and functions to infer CNA from scRNA-seq data. It comes with a companion R package that works as an interface and provides preprocessing, simulation and visualization routines. We suggest to use the R package directly as this serves mosttly as a backend for computations.

Currently providing:

• A mixture model on segments where CNV are modelled as LogNormal random variable (MixtureGaussian)

• A mixture model on segments where CNV are modelled as Categorical random variable (MixtureCategorical)

• A simple Hmm where CNVs are again categorical, but there is no clustering (SimpleHmm)

To install:

$ pip install congas-old

To run a simple analysis on the example data

import congas as cnfrom congas.models import MixtureGaussiandata_dict = cn.simulation_dataparams, loss = cn.run_analysis(data_dict,MixtureGaussian, steps=200, lr=0.05)