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The sequence data were analyzed as a trio, and variants analysis was performed using ClinLabGeneticist software based on the following inheritance patterns: de novo, autosomal recessive.
The sequence data were analyzed as a trio, and variants analysis was performed using ClinLabGeneticist software based on the following inheritance patterns: de novo, autosomal recessive and X-linked, and two de novo variants were identified.
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Variant analysis was performed using the GATK (software.broadinstitute.org) software following the RNA-seq best practices.
Variant analysis was followed by structure formation of haplotypes based on multiple SNPs using SAS software revealed a large number of haplotypes.
The biological context filter in ingenuity variant analysis was applied to downstream data with "Schizophrenia, Neurological Disease and diseases consistent with those two phenotypes" as the filtering criteria.
A multi-variant analysis was also performed by comparing the observed likelihood ratio test statistic from adjusted models with and without the two ATIC variant-by-multivitamin interaction terms with a null distribution of test statistics generated by permuting case status 10,000 times.
Qiagen Ingenuity variant analysis was performed by a contributing scientist.
Variant analysis was performed with samtools 0.1.14 [ 57], annotation of variants was performed with seqgene v 2.3 [ 58].
Our study provided supporting evidence that the application of Cohen's h for rare variant analysis was appealing.
Mutation analysis was performed by MuTect [ 4] and SomaticIndelDetector, copy number variant analysis was performed by ReCapSeg, and rearrangement analysis was performed by BreaKmer [ 1].
Although age was applied as a covariant and the multiple variant analysis was performed in an age-adjusted way, the present results should be interpreted with care.
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