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The former pipeline utilizes the method implemented in the R package DESeq to reveal differential expressed genes between two groups of given RNA samples [ 25].
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Add-on preprocessing of a new patient sample was done utilizing the size factor method implemented in the DESeq2 Bioconductor package [ 24].
"Increased access is going to definitely allow people to utilize the method".
Therefore, to reach improved stringency in CNV calling and to utilize methods implemented in both ExomeCopy and ExomeDepth, we designed an algorithm (ExCopyDepth) combining these two programs (Flow and implementation of ExCopyDepth; Additional file 1: Figure S2).
The second prediction method, implemented in the RNAz program, utilizes information on both conserved secondary structure and thermodynamic stability to identify RNA secondary structures in multiple sequence alignments [12].
The Bayesian method implemented by NEWHYBRIDS 1.1.
This method utilizes the Euler Maruyama method.
Our method, implemented in the new software package anytag, utilizes a nested set of paired-end libraries with decreasing insert sizes.
Developing the RBO method through this software application leads to the important advantage of utilizing new advanced structural reliability methods implemented in OpenSees without compiling the source code.
Relationships between variables were analyzed utilizing the least squares regression, loess estimation and the Pearson or Spearman rank correlation methods implemented in R with default parameters.
The method was implemented experimentally.
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