Clustering and Inference of Copy-Number variations from RNA¶
RNA CNVs Inference and Clustering¶
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: - 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 anneal
To run a simple analysis on the example data
import anneal as an
data_dict = an.load_simulation_seg("data", "example1")
params, loss = an.run_analysis(data_dict,MixtureGaussian, steps=200, lr=0.05)
Warning
package is still under developmet