congas-old 0.0.4

Copy Number genotyping from single cell RNA sequencing

# Copy number genotyping from scRNA sequencing

[](https://travis-ci.org/Militeee/congas) [](https://codecov.io/gh/Militeee/congas)

A set of Pyro models and functions to infer CNA from scRNA-seq data. It comes with a companion [R package](https://github.com/caravagnalab/rcongas) 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

To run a simple analysis on the example data

`python import congas as cn from congas.models import MixtureGaussian data_dict = cn.simulation_data params, loss = cn.run_analysis(data_dict,MixtureGaussian, steps=200, lr=0.05) `