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ncaptier committed Oct 29, 2022
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Expand Up @@ -27,29 +27,29 @@ pip install git+https://github.com/ncaptier/stabilized-ica.git

We provide three jupyter notebooks for an illustration with transcriptomic data :

* [ICA decomposition with stabilized ICA](https://github.com/ncaptier/stabilized-ica/blob/feature_sklearn_api/examples/transcriptomic_ICA.ipynb)
* [Stability of ICA components accross several NSCLC cohorts](https://github.com/ncaptier/stabilized-ica/blob/feature_sklearn_api/examples/stability_study.ipynb)
* [Stabilized ICA for single-cell expression data (cell cycle)](https://github.com/ncaptier/stabilized-ica/blob/feature_sklearn_api/examples/cell_cycle_ICA.ipynb)
* [ICA decomposition with stabilized ICA](https://github.com/ncaptier/stabilized-ica/blob/master/examples/transcriptomic_ICA.ipynb)
* [Stability of ICA components accross several NSCLC cohorts](https://github.com/ncaptier/stabilized-ica/blob/master/examples/stability_study.ipynb)
* [Stabilized ICA for single-cell expression data (cell cycle)](https://github.com/ncaptier/stabilized-ica/blob/master/examples/cell_cycle_ICA.ipynb)

We provide one jupyter notebook for an illustration with EEG/MEG data :

* [Detecting artifacts and biological phenomena on MEG data with stabilized-ica](https://github.com/ncaptier/stabilized-ica/blob/feature_sklearn_api/examples/sica_MEG.ipynb)
* [Detecting artifacts and biological phenomena on MEG data with stabilized-ica](https://github.com/ncaptier/stabilized-ica/blob/master/examples/sica_MEG.ipynb)

We provide one jupyter notebook for an illustration of the integration of stabilized-ica into scikit-learn Machine learning pipelines:

* [MNIST classification with stabilized-ica and multinomial logistic regression](https://github.com/ncaptier/stabilized-ica/blob/feature_sklearn_api/examples/MNIST_classification.ipynb)
* [MNIST classification with stabilized-ica and multinomial logistic regression](https://github.com/ncaptier/stabilized-ica/blob/master/examples/MNIST_classification.ipynb)

## Data

The data set which goes with the jupyter
notebook ["ICA decomposition with stabilized ICA"](https://github.com/ncaptier/stabilized-ica/blob/feature_sklearn_api/examples/transcriptomic_ICA.ipynb)
notebook ["ICA decomposition with stabilized ICA"](https://github.com/ncaptier/stabilized-ica/blob/master/examples/transcriptomic_ICA.ipynb)
can be found in the .zip
file [data.zip](https://github.com/ncaptier/stabilized-ica/blob/feature_sklearn_api/examples/data.zip).
file [data.zip](https://github.com/ncaptier/stabilized-ica/blob/master/examples/data.zip).
Please extract locally the data set before running the notebook.

For the jupyter
notebooks ["Stability of ICA components accross several NSCLC cohorts"](https://github.com/ncaptier/stabilized-ica/blob/feature_sklearn_api/examples/stability_study.ipynb)
and ["Stabilized ICA for single-cell expression data (cell cycle)"](https://github.com/ncaptier/stabilized-ica/blob/feature_sklearn_api/examples/cell_cycle_ICA.ipynb)
notebooks ["Stability of ICA components accross several NSCLC cohorts"](https://github.com/ncaptier/stabilized-ica/blob/master/examples/stability_study.ipynb)
and ["Stabilized ICA for single-cell expression data (cell cycle)"](https://github.com/ncaptier/stabilized-ica/blob/master/examples/cell_cycle_ICA.ipynb)
please note that you will have to load the data yourself in order to run them (all the necessary links are reported on
the notebooks).

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