Metadata-Version: 1.1
Name: congas
Version: 0.0.58
Summary: Copy Number genotyping from single cell RNA sequencing
Home-page: https://github.com/Militeee/congas
Author: Salvatore Milite
Author-email: militesalvatore@gmail.com
License: GPL-3.0
Description: # 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/)
        
Keywords: scRNA scDNA RNA CNV CNA Cancer Copy-number Bioinformatics
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python :: 3.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
