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A set of Pyro models and functions to infer CNA from scRNA-seq data

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# Copy number genotyping from scRNA sequencing

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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-old`

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)
```

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