Copy number genotyping jointly from scRNA and scATAC sequencing

A set of Pyro models and functions to infer CNA from scRNA-seq and scATAC-seq data. It comes with a companion R package that works as an interface and provides preprocessing, simulation and visualization routines.

Currently providing:

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

<!--Coming soon: - A linear model in the emission that can account for known covariates - The equivalent of MixtureGaussian but with CNVs as Categorical random variable - A model on genes (all the other models assume a division in segments) -->

To install:

$ pip install git+https://github.com/caravagnalab/CONGASp

<!-- 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) ``` [Full Documentation](https://annealpyro.readthedocs.io/en/latest/) -->