Metadata-Version: 1.2
Name: scale_v2
Version: 2.0.1.dev0
Summary: Single-cell integrative Analysis via Latent feature Extraction
Home-page: https://github.com/jsxlei/scale_v2
Author: Lei Xiong
Author-email: jsxlei@gmail.com
License: MIT
Description: # SCALE v2: Single-cell integrative Analysis via latent Feature Extraction 
        
        ## Installation  	
        #### install from PyPI
        
            pip install scale-v2
            
        #### install from GitHub
        
        	git clone git://github.com/jsxlei/scale_v2.git
        	cd scale_v2
        	python setup.py install
            
        SCALE v2 is implemented in [Pytorch](https://pytorch.org/) framework.  
        Running SCALE v2 on CUDA is recommended if available.   
        Installation only requires a few minutes.  
        
        ## Quick Start
        
        
        ### 1. Command line
        
            SCALE.py --data_list data1 data2 --batch_categories batch1 batch2 
            
            data_list: data path of each batch of single-cell dataset
            batch_categories: name of each batch
            
        
        #### Output
        Output will be saved in the output folder including:
        * **checkpoint**:  saved model to reproduce results cooperated with option --checkpoint or -c
        * **adata.h5ad**:  preprocessed data and results including, latent, clustering and imputation
        * **umap.png**:  UMAP visualization of latent representations of cells 
        * **log.txt**:  log file of training process
        
             
        #### Useful options  
        * output folder for saveing results: [-o] or [--outdir] 
        * filter rare genes, default 3: [--min_cell]
        * filter low quality cells, default 600: [--min_gene]  
        * select the number of highly variable genes, keep all genes with -1, default 2000: [--n_top_genes]
        	
            
        #### Help
        Look for more usage of SCALE v2
        
        	SCALE.py --help 
            
            
        ### 2. API function
        
            from scale import SCALE
            adata = SCALE(data_list, batch_categories)
            
        Function of parameters are similar to command line options.
        Output is a Anndata object for further analysis with scanpy.
            
        #### Tutorial
        
        See document 
        
        
        ## Previous version [SCALE](https://github.com/jsxlei/SCALE)
        
        SCALE is still available in SCALE v2
        
        ### Command line
        
            SCALE.py --d data --version 1
            
        ### API
        
            from scale.extensions import SCALE_v1
            SCALE_v1(data)
            
            
        All the usage is the same with previous SCALE version 1.
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3.7
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX :: Linux
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >3.6.0
