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By using these fragments, five types of analyses were implemented: analyses of multifractal parameters, analyses of molecular parameters, multifractal map of the human genome, chromosomal location of the most multifractal chromosome fragments, and analyses by gene function, gene family, and gene length.
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All of these implemented analyses condense gene-by-sample measurements (gene profiles) to gene-set-by-sample measurements (gene-set profiles), which are gene-coverage-difference tolerable and free of gene-set size preference for gene-sets with five or more genes (Supplementary Figs S4A, S6A, and S8A).
RRG and JP implemented analyses.
We implemented more analyses of the relationship between Hog1 response and the profiles of different up-staircase/ramp inputs of osmotic stress.
Logistic regression was implemented for analyses of binary outcomes and linear regression for continuous outcomes.
With the availability of an increasing number of closely related or intraspecific prokaryotic genomes, as well as the advent of whole-genome alignment algorithms [ 11, 12], there is an opportunity to implement phylogenomic analyses of the evolution and ecological adaptation of these organisms on the whole-genome scale.
Consequently, we have also implemented coalescent-based analyses of effective migration in addition to more traditional distance-based analyses.
A sequential threshold-linear censored model was implemented for the analyses of SURV.
For data analysis, linear mixed effects models [ 43] were implemented in all analyses of variance (ANOVAs) using SAS 9.1 [ 44].
Standard LC methods performed under acidic conditions as well as tandem mass spectrometry can be implemented in future analyses of phosphorylation sites.
The NJ and minimum evolution methods utilized the BIONJ (42) and balanced fastME (43) functions, correspondingly, as implemented in the Analyses of Phylogenetics and Evolution (ape) library (61) for R. The data were visualized online and were exported using built-in functionality provided in ape.
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