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In highly heritable phenotypes, above 60%, a genome-wide scan was implemented using a modified version of the Haseman and Elston method [31] in a generalised linear model in which the square of the sibling differences was regressed on estimated identical-by-descent (IBD) status at each locus [32].
The HABC procedure was implemented using a modified version of the MSBAYES comparative phylogeographic software pipeline [ 35, 36] consisting of several C and R programs that are run with a Perl "front-end" and utilizes a finite sites version of Hudson's classic coalescent simulator [ 45].
The visualization of 3D small molecule conformations and biological assemblies has been implemented using a modified version of GLmol (http://webglmol.sourceforge.jp), which itself uses WebGL, a pure JavaScript API supported by most modern browsers to render 2D and 3D graphics (http://www.khronos.org/webgl).org/webgl
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All but optimal matching methods were implemented using a modified SAS® Macro based on Coca-Perraillon [ 20].
The simulations were implemented in Java using a modified version of the program Antigen (http://bedford.io/projects/antigen/).io/projects/antigen/
Second, the factors were selected following a parallel analysis implemented in SAS using a modified version of the Kabacoff's code [ 33].
Differentially methylated regions (DMRs) were identified using a modified version of the champ.lasso function implemented in the R package ChAMP [ 73].
This distance matrix is calculated by comparing two sequence trees at the base/base-pair level (as in Fig. 6) by using a modified version of the tree-edit algorithm implemented in RNAdist of the ViennaRNA package.
The in situ hybridization screening protocol was implemented to score nuclear foci on a Molecular Devices Micro plate reader using a modified version of the granularity analysis journal.
Raw Agilent V3 miRNA data were preprocessed using a modified version of Robust Multi-array Analysis (RMA)[ 41] without background correction, implemented in the AgiMicroRna R package [ 42].
Tag SNPs were chosen using a modified version of the method described by Carlson et al. (2004) as implemented in the Tagzilla module of the GLU software package, version 1.0b2 (Jacobs 2010).
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