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Then an attenuation map was generated using the algorithm implemented in the scanner software, assuming the tissue attenuation coefficient value to be uniform [9].
Recombination rates were inferred directly from sequence data using the algorithm implemented in LDhat [48].
For this experiment, we decided to use a random forests algorithm (RF) as a base classifier (we are using the algorithm implemented in [3] for reproducibility purposes), generating 150 trees.
PCA was performed using the algorithm implemented in MATLAB, R2009b (MathWorks, Natick, MA, USA).
Multi-class significance analysis (SAM) was done using the algorithm implemented in MeV from TM4 software.
Data were analyzed, using the algorithm implemented in the statistical package qpcR (version 1.3-6) (Ritz and Spiess 2008).
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The graph is constructed using the algorithms implemented in the Minia assembler (Chikhi and Rizk, 2013; Salikhov et al., 2013).
Using the algorithms implemented in TOPP/OpenMS [ 28, 31], we performed peptide feature detection, alignment and statistical analysis for these runs.
In silico functional profiling of target genes Potential miRNA target genes were identified and retrieved using the algorithms implemented by the Sanger microRNA database [ 25] and by TargetScan 4.2 [ 26].
The Gaussian kernel density function shown in Figure 1 uses the algorithm implemented in the R density function.
For population assignment analysis we used the algorithm implemented in the program STRUCTURE 2.3 [ 21] coding phased sequences as alleles, including only individuals with a complete nuclear dataset (3 nuclear fragments).
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