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Description:
magicimpute 3.0.0
Markov Affinity-based Graph Imputation of Cells (MAGIC) is an algorithm for denoising high-dimensional data most commonly applied to single-cell RNA sequencing data. MAGIC learns the manifold data, using the resultant graph to smooth the features and restore the structure of the data.
To see how MAGIC can be applied to single-cell RNA-seq, elucidating the epithelial-to-mesenchymal transition, read our publication in Cell.
David van Dijk, et al. Recovering Gene Interactions from Single-Cell Data Using Data Diffusion. 2018. Cell.
For R and MATLAB implementations of MAGIC, see
https://github.com/KrishnaswamyLab/MAGIC.
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.
License
For personal and professional use. You cannot resell or redistribute these repositories in their original state.
Files:
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