Metadata-Version: 2.1
Name: congas-old
Version: 0.0.4
Summary: Copy Number genotyping from single cell RNA sequencing
Home-page: https://github.com/Militeee/congas
Author: Salvatore Milite
Author-email: militesalvatore@gmail.com
License: GPL-3.0
Keywords: scRNA scDNA RNA CNV CNA Cancer Copy-number Bioinformatics
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python :: 3.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
License-File: LICENSE

# Copy number genotyping from scRNA sequencing


[![Build Status](https://travis-ci.org/Militeee/anneal.svg?branch=master)](https://travis-ci.org/Militeee/congas)
[![codecov](https://codecov.io/gh/Militeee/anneal/branch/master/graph/badge.svg)](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)
```


