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The ICV for each individual was calculated using a stereologic Cavalieri technique [ 33] implemented through MEASURE software.
First, the number of EM risk alleles carried per individual was calculated using the 'score' command in PLINK.
The probability of concurrent DNA changes in the same individual was calculated using the Poisson distribution [ 44].
The number of contiguous homozygous SNPs required for significance in relation to the degree of consanguinity for each individual was calculated using an algorithm adapted from a previous study (35).
The cumulative genetic risk for each individual was calculated using the estimated regression coefficients of the 350 markers included in the model, providing a measure of the extent to which common allelic variation (and the variables in the model) explained disease status in this dataset.
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Statistical comparisons between tissue pairs in each individual were calculated using the Wilcoxon Rank Sums test.
Baseline faecal stress hormone metabolite concentrations for each individual were calculated using the remaining samples in the 'low' stress level category collected throughout the broader study period.
Statistical comparisons between PL and BM in each individual were calculated using the Wilcoxon Rank Sums test, while statistical comparisons between PL and BM for pooled data were performed using a Generalized Estimating Equations (GEE) model accounting for repeated measures from multiple subjects.
Secondary parameters for each individual were calculated using maximum a posteriori Bayesian estimates for each individual.
Copy numbers in each individual were calculated using the 2−ΔΔCt method.
Haplotypes and haplotype frequencies per individual were calculated using the program SNPHAP (http://wwwgene.cimr.cam.ac.uk/clayton/software).ac.uk/clayton/software
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