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Usable statistics (see Table 2 for list of currently available statistics) implement the MafStatistics interface.
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The package adopts the linear modeling approach implemented by lmFit and the empirical Bayesian statistics implemented by eBayes.
To understand population differentiation within T. cacao and to overcome the problem of mislabeled samples, we conducted a study using Bayesian statistics implemented through the software Structure [12].
Admixture proportions were estimated with mY statistics implemented in Admix 2.0.
The phylogenetic tree for the dataset was estimated using Bayesian statistics implemented in MrBayes 3.1.2 [ 35].
All output measurements are analyzed using MATLAB and statistics implemented using custom R scripts.
The Bayesian regression approach implemented in BAYESCAN has several advantages over the widely used approach based on summary statistics implemented in FDIST2 [ 56].
To avoid such a problem, we used the agglomeration analysis implemented in the PAST software [ 62] and Bayesian statistics implemented in the Structure program [ 56].
The spatial scan statistics implemented in SaTScan software [ 45] were used to carry out a cluster analysis to determine the spatial aggregation of infant mortality.
Differential methylation analysis was performed after adjusting the data for smoking, using empirical Bayes paired moderated t statistics implemented in the R package limma [ 99].
The list of statistically significant differentially expressed genes was obtained by applying the linear modeling approach implemented in lmFit package for Python and the empirical Bayes statistics implemented by eBayes from the limma R package (http://bioinf.wehi.edu.au/limma/; [ 16]).
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