ylaboratory / ALPINE-analysis

This repository contains the demo and source code used in the ALPINE. If you want to learn more about the ALPINE, follow the link below.

ALPINE-analysis

This repository provides the code used to analyze data for the ALPINE paper and includes extensive information on the ALPINE package. The repository is organized as follows:

Folder Name	Description
data	Contains the raw data used in the paper or links to download it.
src	Includes scripts and notebooks for data analysis.
tutorials	Provides tutorials for data analysis and model optimization.

a. tutorials

directory	description
tutorials/ComponentOptimizer	contains some tutorials for the optimization of the ALPINE model
tutorials/ALPINE	contains the code for the ALPINE package
tutorials/tutorial.ipynb	the jupyter note covers the optimization and excution of the ALPINE using the simulation dataset
tutorials/transfer_from_anndata_to_Seurat	In this file, we demonstrate how to easily transfer the ALPINE data to the Seurat Object for your downstream analysis.

b. src

directory	description
src/simulation	contains the codes for the simulation study (including analysis and data simulation)
src/benchmark	contains the benchmark codes
src/case_studies	contains the case studies codes

c. data

directory	description
data/tutorial_simulation	provides the necessary zipped data for the tutorial.