From 0ce2e25968cac7102f50a734c56221c54c4a8dbe Mon Sep 17 00:00:00 2001
From: Christophe  BOETTO <cboetto@pasteur.fr>
Date: Wed, 12 Jun 2024 16:01:26 +0200
Subject: [PATCH] clarified readme, and added pinned commit for BiB article

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 # Gitlab repository for the MANOCCA project
 
-Tool used to compute the covariance test on a set of predictors, presented in this paper : hhttps://academic.oup.com/bib/article/25/4/bbae272/7690346 MANOCCA (Multivariate ANalysis of Conditional CovAriance) performs the covariance test : $Cov(Y_1,Y_2) ~ X + C$, as well as the multivariate version with more than two Y outcomes. In quick words, MANOCCA (Multivariate ANalysis of Conditional CovAriance) is a test of differences of covariance with regard to a predictor. The test is orthogonal to mean and variance effects, and will only grasp covariance effects.
+Tool used to compute the covariance test on a set of predictors, presented in this paper : https://academic.oup.com/bib/article/25/4/bbae272/7690346 MANOCCA (Multivariate ANalysis of Conditional CovAriance) performs the covariance test : $Cov(Y_1,Y_2) \~ X + C$, as well as the multivariate version with more than two Y outcomes. In quick words, MANOCCA (Multivariate ANalysis of Conditional CovAriance) is a test of differences in correlations/covariance with regard to a predictor. The test is orthogonal to mean and variance effects, and will only grasp covariance effects.
+
+One application of the MANOCCA test to detect co-abunding human gut microbiome communities can be found in this preprint : https://www.medrxiv.org/content/10.1101/2024.04.30.24306630v1.full
+
+Note : If all outcomes are centered and scaled, then $Corr(Y_1, Y_2) = Cov(Y_1,Y_2)$ and MANOCCA can test for changes in correlation. The subtleties of covariance vs correlation are discussed in the main draft and supplements of the paper above. 
 
 Author : Christophe BOETTO
 
+Archived commit pinned for the article https://academic.oup.com/bib/article/25/4/bbae272/7690346 in case the tool evolves in the future : 6d76df07
+To go to this specific commit do :
+- git clone <manocca_https_link>
+- cd manocca
+- git reset --hard 6d76df07
+
 
 # Contents
-The current repository contains the Python and R versions of MANOCCA. The python is more detailed than the R version, but I will work on it.
+The current repository contains the Python and R versions of MANOCCA. The python is more detailed than the R version, but they both provide the same test. 
 In the Python version you will find :
 - MANOCCA - the multivariate test on covariance
 - MANOVA - the multivariate test on mean
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