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Any region where the smooth density profile exceeded a fixed threshold, relative to the uniform background of the total confident read count divided by the genome size, was considered enriched.
A region was considered enriched if it consisted of at least four probes, none of which were more than 600 bases apart, with at least 66% of the probes exhibiting enrichment over threshold.
A region was considered enriched if it contained at least 10 sequences, none separated by more than 100 bases, and the total number of sequences in the region exhibited at least a 5-fold enrichment over the number of sequences seen in the same region from an input run.
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Elements were considered enriched if they displayed an enrichment of at least a ±1.5 fold change and had a P-value < = 0.05.
Functional categories were considered enriched when the –log scale geometric mean p-value ≤ 0.05 (enrichment score ≥ 1.3).
Terms with P values adjusted for multiple testing ≤ 0.01 were considered enriched.
The second reason is that our mice are routinely kept in conditions that would, in most labs, be considered "enriched" already.
Functional annotation terms were considered enriched for an Enrichment Score larger than 3, which corresponds to a geometric average p-value of 0.001.
Genes were ranked by fold change calculated using the "difference of class means" metric implemented in the GSEA software, such that genes ranked towards the top of the list are considered enriched in one sample group and genes ranked at the bottom are considered enriched in the other.
Reactome pathways exhibiting FDR values < 0.01 were considered enriched.
Only the pathways with corrected P values less than 0.05 were considered enriched.
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CEO of Professional Science Editing for Scientists @ prosciediting.com