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This technique allows statistical models to be created accounting for data levels, and the probability of data groups coming from the same population of data were inferred by comparing models using analysis of variance comparisons.
Admixture proportions from autosomal data were inferred by comparing genetic profiles from the present study with those publicly available from the Human Genome Diversity Cell Line Panel, HGCP-CEPH (Centre d'Etude du Polymorphisme Humain; [ 94]).
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The most likely value of K, given the data, was inferred by the Evanno et al.
Some of the missing data was inferred by examining the allele calls flanking the missing data for a given line within a scaffold.
Leslie et al. [ 14] developed a statistical method based on identity by descent, which uses phase-resolved genotype data (i.e. full haplotype information was inferred by multiple SNPs) to predict HLA alleles.
Missing data were inferred using the replace missing data by flanking genotypes function, with a maximum probability of double recombination set to 0.001.
Both of their HC data sets were inferred by first removing 44 nonspecific contaminants and nearly all cytoplasmic ribosomal subunits from the raw data.
For the unphased genotype data, haplotypes were inferred by MERLIN [ 25] software, which is commonly used to reconstruct putative haplotypes for families and individuals using likelihood-based methods.
Importantly, many of these high-scored network nodes are not differentially expressed in the microarray data set, but were inferred by the algorithm from the differentially expressed gene pattern and the analysis of network connectivity.
From the expression data of each species, co-expression networks were inferred by computing mutual information (MI) for each gene pair, applying the context likelihood of relatedness (CLR) algorithm to obtain background-corrected Z-score and finally by applying a threshold to decide whether a gene-pair should be linked or not (henceforth referred to as the CLR threshold).
The 95% CIs of parameter estimates were inferred by fitting data sets resampled over SNP positions.
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