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In this study, both datasets were filtered to minimize the impact of the identified GC bias and exclude the artificial duplicate sequences.
All resulting datasets were filtered using the absolute call metric (present or absent) implemented within Microsoft Access (Microsoft Corporation, Redmond, WA).
Both datasets were filtered to exclude essential genes, as well as all genes not found to participate in any synthetic-lethality relationships.
In the process of LD estimation, SSR datasets were filtered for rare alleles with frequencies of less than 5% in the whole collection and computed using 100,000 permutations.
Large datasets were filtered to include only regions shown in Figure 1.
All of these datasets were filtered to remove variants contained within the HGMD or ENCODE training and validation datasets.
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Previously annotated AS events in our dataset were filtered out by comparing sequences with ASTD version 1.1 and IPI version 3.16 using Washington University basic local alignment search tool (WU-BLAST) version 2.0, applying the pam30 substitution matrix.
Genes in the GDS1813 dataset were filtered by requiring a "present" flag in at least 30 out of 52 samples.
Gene expression data were used as provided and probe sets with low expression or low variation across the dataset were filtered as described in the Methods.
On the basis of the prior belief that RP-related mutations are rare; calls with minor allele frequencies greater than 0.5% in the 1000 genomes dataset were filtered.
Clusters without any small RNAs in the Miwi2 −/− dataset, and in the bottom quartile of density in the WT dataset, were filtered because they were too small to determine MIWI2 dependence.
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