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CNVs in the genome data were detected using RDXplorer [ 41] and filtered with a customized pipeline.
The present genes (represented by probe-sets of Affymetrix Gene Chips®) of our microarray data were detected using Affymetrix MAS5 method implemented in Bioconductor packages.
Non-homogeneities in the data were detected using residual analysis as described elsewhere [ 27]. 2 × 2 crossover ANOVA was used for data evaluation.
Outliers in microarray data were detected using criterion of z > 7 for log-transformed Cy3 and Cy5 data separately and removed (0.17% of the data).
SSRs in the read data were detected using a Perl script in the Simple Sequence Repeat Identification Tool (SSRIT), with minimum thresholds of nine, six, five, five, five, and five repeat units for di-, tetra-,etra-, penta-, hexa-, and heptanucleotide repeats, respectively.
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A change in paired data was detected using Wilcoxon matched-pairs signed-rank test.
For each regression model, autocorrelation of the data was detected using the Durbin-Watson test and corrected using general least squares regression [ 25, 6].
For this set of proteins, homologs among all the viral proteomes together with homologs with the largest coverage relating to our inquiry in environmental sequence data (env_nr) were detected using BLASTP.
Myogenic DMRs from the same RRBS data sets were detected using our UPQ algorithm as recently described.
As a result, one locus showing significant imprinting effect was detected in the Imp data (p-value 3.49×10−16) and none were detected using the Dom data, as expected.
In all comparisons, after data normalization and background correction, peaks were detected using the same peak detection procedure used for MAT and TileProbe.
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