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All remaining algorithm parameters were as default settings.
Codon frequencies were estimated from the dataset using the F3 × 4 option, other settings were as default.
Settings for the analysis were as default (e.g. detection above background p-value>0.05, probability statistic: moderated t-test), except that we used a raw expression threshold >45 (∼5.5 log2 value) and a gene expression cut-off >100 to ensure DEX genes to be taken into account.
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Burn-in was as default setting (discarding 25% of samples).
The methodology was as default, except that data rescaling was turned off as it was not required for this binary data set.
The field of «Computer name» is not necessarily needed, you can leave is as default.
Not every sovereign default is as convoluted as Argentina's.
The 100 best solutions were saved; other parameters were kept as default.
In this study, linear and Gaussian kernels were used and the hyperparameters were set as default values in MATLAB functions.
All settings were kept as default except the minimum threshold was set to 60.
The force fields of conformations were further check with CHARMm, and the parameters used were set as default values.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com