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Significance of FST for each locus was based on a test for population differentiation with the log-likelihood G-statistic with the assumption of random mating within samples, implemented in FSTAT.
Differential analysis was then performed using a moderated t test, comparing mean of log2 intensities) in both H3.1- and H3.3-mutated DIPG samples, implemented in the limma R package.
From the outset, the UKHLS strategy involved the collection of a wide range of health-related information, drawing on standard interviewing and data linkage (implemented from wave 1 onward) as well as the collection of physical health measures, blood samples (implemented in waves 2 and 3) and cognitive measures (implemented in wave 3).
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An initial 3D conformation is necessary for using the conformer sampler implemented in BCL Conf.
Samples from the posterior distribution were drawn with Gibbs sampling, implemented in the JAGS Gibbs sampling environment (Plummer 2003).
We draw comparison of MC4Inversion to the sampler implemented in BADGER and a previously described importance sampling (IS) technique.
The random-walk Metropolis sampling implemented in R (R Development Core Team 2005) was tested with simulation.
We employed a Bayesian discrete phylogeographic approach using Markov chain Monte Carlo (MCMC) sampling implemented in the BEAST v1.8.1 software package (Drummond & Rambaut, 2007).
The StatAlign package - a Markov chain Monte Carlo (MCMC) sampler implemented in Java - samples alignment parameters, sequence alignments, tree branch lengths and tree topologies in order to infer both the alignment and the phylogenetic tree relating the input sequences [ 28].
A full Bayesian approach using Markov chain Monte Carlo (MCMC) methods [ 15] via Gibbs sampling implemented in the DMU package [ 16] was used to fit the models and sample posterior PM.
A multiple-sequence alignment was constructed using ClustalW and phylogenetic trees were performed applying the neighbor-joining method with the 1000-bootstrap re-sampling inplementhe in the Molecular Evolutionary Genetics Analysis, version 5.0 program.
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