Jean-Baptiste SCHIRATTI

Adding support for R in ml-hub

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As a data scientist, I use both R and Python and would really appreciate if R (say, version 4.0.3) was part of ML-Hub. Adding R support could be optional (something...

Warnings with Scikit-Learn >= 0.20

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With Scikit-Learn >= 0.20 the examples give rise to the following warning: - with `LogisticRegression` : `FutureWarning: Default solver will be changed to 'lbfgs' in 0.22. Specify a solver to...

User-defined feature functions made easy

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1. I think that `_embed`, `_filt`, `_wavelet_coefs` (in utils.py) should not be private functions and should be added (along with `power_spectrum`) to MNE-features' API. The reason for that is that...

Multiple calls to `power_spectrum`

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``` from mne_features.feature_extraction import extract_features import numpy as np sfreq = 256. rng = np.random.RandomState(seed=42) data = rng.standard_normal((10, 20, int(sfreq))) selected_features = ['pow_freq_bands', 'hjorth_mobility_spect', 'hjorth_complexity_spect', 'spect_entropy'] features = extract_features(data, sfreq,...

Doc-related issues

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Since the last PR, there are warnings when building the doc of MNE-features. ```WARNING: [autosummary] failed to import u'mne_features.univariate.compute_spect_edge': no module named mne_features.univariate.compute_spect_edge``` It seems that Travis is not checking...

FIX: deal with flat epochs in feature extraction

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The function `extract_features` extracts features from a data array `X, shape (n_epochs, n_channels, n_times)` _epoch by epoch_. If an epoch is flat (that is, if np.allclose(X[j, :, :], 0) is...

This PR addresses #179 and adds an example with real data.

In [examples/examples/plot_minimal_pydeseq2_pipeline.py](https://github.com/owkin/PyDESeq2/blob/8fbcc2faf744518852c90552242a5049f5d9c9c8/examples/plot_minimal_pydeseq2_pipeline.py), we plot log-fold change versus mean expression using: ```python stat_res.plot_MA(s=20) ``` Currently, there is no easy way to adjust the `xlim` and `ylim` attributes of the figure displayed....

[FEAT] Add an example with "real data"

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As a PyDESeq2 user, I'd like to have a example/tutorial with "real data" to illustrate PyDESeq2 capabilities. @tobias-zehnder and @Valerieducret might be interested in this!