Copy Number genotyping from single cell RNA sequencing
Project description
# 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
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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