Metadata-Version: 2.1
Name: BLADE-Deconvolution
Version: 0.0.1
Summary: BLADE (Bayesian Log-normAl DEconvolution)
Home-page: https://github.com/tgac-vumc/BLADE
Author: Yongsoo Kim
Author-email: anoyaro84@gmail.com
License: UNKNOWN
Description: <p align="center">
          <img width="231" height="271.5" src="https://github.com/tgac-vumc/BLADE/blob/master/logo_final_small.png">
        </p>
        
        # BLADE: Bayesian Log-normAl DEconvolution
        
        
        BLADE (Bayesian Log-normAl DEconvolution) was designed to jointly estimate cell type composition and gene expression profiles per cell type in a single-step while accounting for the observed gene expression variability in single-cell RNA-seq data. 
        
        Demo notebook is available [here](https://github.com/tgac-vumc/BLADE/blob/master/jupyter/BLADE%20-%20Demo%20script.ipynb).
        
        <p align="center">
          <img width="490" height="820" src="https://github.com/tgac-vumc/BLADE/blob/master/framework.png">
        </p>
        
        
        ## Installation
        
        ### Using Conda
        ### Step 1: Installing Miniconda 3
        First, please open a terminal or make sure you are logged into your Linux VM. Assuming that you have a 64-bit system, on Linux, download and install Miniconda 3 with:
        
        ```
        wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
        bash Miniconda3-latest-Linux-x86_64.sh
        ```
        On MacOS X, download and install with:
        
        ```
        curl https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -o Miniconda3-latest-MacOSX-x86_64.sh
        bash Miniconda3-latest-MacOSX-x86_64.sh
        ```
        
        ### Step 2: Create a conda environment
        
        You can install all the necessary dependency using the following command.
        
        ```
        conda install mamba -c conda-forge -y
        mamba create --name BLADE -c conda-forge -c bioconda jupyter numpy numba scikit-learn joblib multiprocess time scipy qgrid seaborn
        ```
        
        Then, the `BLADE` environment can be activate by:
        
        ```
        conda activate BLADE
        ```
        
        ### Using Singularity
        
        If you have Singularity, you can simply pull the singularity container with all dependency resolved.
        
        ```
        singularity pull shub://tgac-vumc/BLADE
        ```
        
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
