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For analyses of both datasets, we excluded all indels and only nucleotide mutations were considered.
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For all three datasets we excluded individuals <2 years old and pregnant women because obesity definitions are not applicable to them.
For our final dataset, we excluded all non-European breeds as well as breeds that are known to have been introduced to various European islands in recent times.
To increase the confidence in the interaction dataset, we excluded all the interactions inferred through homology.
From the initial 26 centres included in the dataset, we excluded 7 centres based on these criteria.
Using these statistical methods on a large, validated dataset, we excluded depth as a prognostic factor and established that age, duration of symptoms, size, grade, margin, and radiotherapy were important prognostic factors for both local recurrence and disease-specific mortality.
As for the bladder cancer dataset, we excluded the sexual chromosomes from the analysis, resulting in a total of 3649 spots.
From this dataset, we excluded by sequence comparison against SwissProt and reference searches, 75 proteins annotated as terminators, antiterminators, and sigma factors, among others.
For the Phase 3 dataset, we exclude rare variants that are present in only one individual.
Genes not included in both datasets were excluded from the analysis.
Since rMATS requires all input datasets to have the same read length, we excluded the dataset from E15.5 which had a different read length compared to others.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com