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Copy Number genotyping from single cell RNA sequencing

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# 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 (hlink) that works as an interface and provides preprocessing, simulation and visualization routines.

Currently providing:

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

  • Same as above but the number of cluster is learned (MixtureGaussianDMP)

  • A model where CNVs are modelled as outcome from Categorical distributions, clusters share the same parameters (MixtureDirichlet)

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

  • The version of MixtureDirichlet but with temporal dependency (HmmMixtureRNA)

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 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) `

[Full Documentation](https://annealpyro.readthedocs.io/en/latest/)

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