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The CFPM, though, can easily be run using other, statistical software such as Stata [ 22].
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ExomeWalker was run using the other genes in the phenotypic series as seed genes for the random walk.
The minimus2 pipeline [ 11], a lightweight assembler which is part of the AMOS package, was run using REFCOUNT = 0 (other parameters default).
Consider if samples were run in strata of starting RNA, e.g. we have an experiment where some samples were run using 250 ng, while others were run using 50 ng.
MACS (version 1.4.0rc2) was run directly using Python, whereas the other methods were run using their implementations in the 'chipseq' R package, with the command ' estimate.mean.fraglen'.fraglen'
The other methods were run using the default values of the parameters.
All models were run in R 2.8.1 software [40], [41] whereas all other statistical analyses were run using SPSS 15.0.1.
Experiments were run using custom software.
Analyses were run using SPSS.
The simulations were run using R V.3.1.2.
Interpro was run using its default cutoffs.
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