Clustering and Inference of Copy-Number variations from RNA

Copy number genotyping from scRNA sequencing

A set of Pyro models and functions to infer CNA from scRNA-seq data. It comes with a companion R package (in progress) 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: - NUTS support

To install:

$ pip install congas

To run a simple analysis on the example data

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)

Warning

package is still under developmet

Indices and tables