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The dataset SNPs from the top scoring 200 models included 92 intragenic SNPs mapping to 77 genes.
We compared the proportion of top genes identified in individual datasets with the top genes from the meta-analysis, using Correspondence At the Top (CAT) plots [ 17].
Similar to the cancer/reference dataset, 23 of the top 100 genes ranked by probe fold change from the progression dataset are homeobox genes (Table 2).
From the experiments conducted on three sample datasets, the top 15 communities from all the datasets were ascertained, with the graphical representation.
Similarly, mul-DT improved the accuracy of DT from 64.8% to 84.1% in the Pros.2 dataset using the top 0.4% genes; from 84.9% to 100% in the Pros.3 dataset with the top 0.4% genes; and from 80.5% to 97.4% in the DLBCL dataset with the top 1% genes.
Supporting evidence was also found for additional genes from the top 30 dataset SNPs.
When a dataset is examined in comparison with a reference, the pipeline produces a figure with allelic ratios for the reference strain drawn as grey lines emanating from the bottom of the cartoon and allelic ratios for the test dataset plotted as red lines drawn from the top of each chromosome.
The same evaluations were performed again using the oversampled dataset and the top 20 uncorrelated sets of features, including the top five uncorrelated features from the five main regions of the brain.
From each dataset, we identified the top 400 exonic ASE SNPs using the naive Bayes statistics.
For testing cluster robustness, we used a re-sampling approach in which we randomly excluded five samples from the dataset, then selected the top 40% highest variance genes and performed clustering using the partitioning around medoids (PAM) algorithm with k = 5.
MYOTUBE_UP and MYOTUBE_DOWN are control genelists derived from the top 250 up- or down-regulated genes derived directly from the myotube dataset.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com