Metadata-Version: 2.1
Name: magic-impute
Version: 1.5.1
Summary: MAGIC
Home-page: https://github.com/KrishnaswamyLab/MAGIC
Author: 
Author-email: 
License: GNU General Public License Version 2
Download-URL: https://github.com/KrishnaswamyLab/MAGIC/archive/v1.5.1.tar.gz
Description: =======================================================
        Markov Affinity-based Graph Imputation of Cells (MAGIC)
        =======================================================
        
        .. image:: https://img.shields.io/pypi/v/magic-impute.svg
            :target: https://pypi.org/project/magic-impute/
            :alt: Latest PyPi version
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            :target: https://cran.r-project.org/package=Rmagic
            :alt: Latest CRAN version
        .. image:: https://api.travis-ci.com/KrishnaswamyLab/MAGIC.svg?branch=master
            :target: https://travis-ci.com/KrishnaswamyLab/MAGIC
            :alt: Travis CI Build
        .. image:: https://img.shields.io/readthedocs/magic.svg
            :target: https://magic.readthedocs.io/
            :alt: Read the Docs
        .. image:: https://zenodo.org/badge/DOI/10.1016/j.cell.2018.05.061.svg
            :target: https://www.cell.com/cell/abstract/S0092-8674(18)30724-4
            :alt: Cell Publication DOI
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            :target: https://twitter.com/KrishnaswamyLab
            :alt: Twitter
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            :alt: GitHub stars
        
        Markov Affinity-based Graph Imputation of Cells (MAGIC) is an algorithm
        for denoising and imputation of single cells applied to single-cell RNA
        sequencing data, as described in Van Dijk D *et al.* (2018), *Recovering
        Gene Interactions from Single-Cell Data Using Data Diffusion*, Cell
        https://www.cell.com/cell/abstract/S0092-8674(18)30724-4.
        
        For R and MATLAB implementations of MAGIC, see
        https://github.com/KrishnaswamyLab/MAGIC.
        
        
        .. image:: https://raw.githubusercontent.com/KrishnaswamyLab/MAGIC/master/magic.gif
            :align: center
            :alt: Magic reveals the interaction between Vimentin (VIM), Cadherin-1 (CDH1), and Zinc finger E-box-binding homeobox 1 (ZEB1, encoded by colors).
        
        *Magic reveals the interaction between Vimentin (VIM), Cadherin-1
        (CDH1), and Zinc finger E-box-binding homeobox 1 (ZEB1, encoded by
        colors).*
        
        Installation
        ~~~~~~~~~~~~
        
        Installation with pip
        ---------------------
        
        To install with ``pip``, run the following from a terminal::
        
           pip install --user magic-impute
        
        Installation from GitHub
        ------------------------
        
        To clone the repository and install manually, run the following from a
        terminal::
        
           git clone git://github.com/KrishnaswamyLab/MAGIC.git
           cd MAGIC/python
           python setup.py install --user
        
        Usage
        ~~~~~
        
        Example data
        ------------
        
        The following code runs MAGIC on test data located in the MAGIC
        repository::
        
           import magic
           import pandas as pd
           import matplotlib.pyplot as plt
           X = pd.read_csv("MAGIC/data/test_data.csv")
           magic_operator = magic.MAGIC()
           X_magic = magic_operator.fit_transform(X, genes=['VIM', 'CDH1', 'ZEB1'])
           plt.scatter(X_magic['VIM'], X_magic['CDH1'], c=X_magic['ZEB1'], s=1, cmap='inferno')
           plt.show()
           magic.plot.animate_magic(X, gene_x='VIM', gene_y='CDH1', gene_color='ZEB1', operator=magic_operator)
        
        Interactive command line
        ------------------------
        
        We have included two tutorial notebooks on MAGIC usage and results
        visualization for single cell RNA-seq data.
        
        EMT data notebook:
        http://nbviewer.jupyter.org/github/KrishnaswamyLab/magic/blob/master/python/tutorial_notebooks/emt_tutorial.ipynb
        
        Bone Marrow data notebook:
        http://nbviewer.jupyter.org/github/KrishnaswamyLab/magic/blob/master/python/tutorial_notebooks/bonemarrow_tutorial.ipynb
        
        Help
        ~~~~
        
        If you have any questions or require assistance using MAGIC, please
        contact us at https://krishnaswamylab.org/get-help.
        
Keywords: visualization,big-data,dimensionality-reduction,embedding,manifold-learning,computational-biology
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Framework :: Jupyter
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: Natural Language :: English
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Provides-Extra: doc
Provides-Extra: test
