congas

Name	congas JSON
Version	0.0.78 JSON
	download
home_page	https://github.com/Militeee/congas
Summary	Copy Number genotyping from single cell RNA sequencing
upload_time	2023-10-03 10:11:09
maintainer
docs_url	None
author	Salvatore Milite
requires_python
license	GPL-3.0
keywords	scrna scdna rna cnv cna cancer copy-number bioinformatics
VCS
bugtrack_url
requirements	No requirements were recorded.
Travis-CI
coveralls test coverage	No coveralls.

            # 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](https://github.com/caravagnalab/rcongas) 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 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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