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Commits on Mar 27, 2020

• Merge pull request #43 from ntraut/master

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  deep-introspection

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• Use numpy for computing propagation

  ntraut

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Commits on Feb 27, 2020

• Correct COO/CSP sparse matrix bug

  

  Guillaume DUMAS

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• Merge pull request #42 from 0m1n0/master

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• addition of the choice between launching the code in a one-time ("full_step") run or in three parts: "preprocessing", "bootstrap", "clustering"

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• Merge branch 'master' of https://github.com/0m1n0/stratipy

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• not used comments removed

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• print function with flush=True

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• variable name changed: "patients" -> "Individuals"

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Commits on Dec 9, 2019

• Update setup.py

  deep-introspection

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• Merge pull request #41 from 0m1n0/master

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  0m1n0

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• Update README.md

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• Merge branch 'master' into master

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• Versionning README.md

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Commits on Dec 5, 2019

• Update to version 0.8

  deep-introspection

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• Merge pull request #39 from 0m1n0/master

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• from binary to weighed mutation profile, based on observed/expected score of gnomAD

  0m1n0

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• only one iteration of propagation, alpha fixed by PPI network edge number

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• PPI network data formatting cleaned

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• variable name changed: patient -> individual

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Commits on May 27, 2019

• individual selection with Admixture model

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• if mut_type == 'raw', there will be no PPI network formatting/application

  0m1n0

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• Quantile normalisation modified using pandas.DataFrame.rank: if found two scores are same then assign the minimum rank to both the score

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Commits on Apr 1, 2019

• Merge pull request #38 from 0m1n0/master

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• more readability

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• reproducibility code uploaded

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Commits on Feb 28, 2019

• STRING PPI file name changed: version added (v9)

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Commits on Jan 8, 2019

• incorrect individual indexing has been corrected: from phenotype individual indexes to mutation profile individual indexes

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Commits on Dec 18, 2018

• Load gene filtered data

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• few minor modifications

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• when bootstrap step is split, all sub-bootstrap files will be removed after merging

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• k=20->50: plot size adapted

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• Go enrichment analysis: GO Slim. Save also significant p-value counts.

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Commits on Dec 17, 2018

• Get NaN when divided by zero

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Commits on Oct 23, 2018

• Mutation type (raw, diff, qn_mean, qn_median) is now directly done by parameter "mut_type" /// Parameter "qn" is removed /// Parameter "alpha" no longer needs the value "0"

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