acorn: an R package forde novovariant analysis

Abstract

Background: The study of de novo variation is important for assessing biological characteristics of new variation and for studies related to human phenotypes. Software programs exist to call de novo variants and programs also exist to test the burden of these variants in genomic regions; however, I am unaware of a program that fits in between these two aspects of de novo variant assessment. This intermediate space is important for assessing the quality of de novo variants and to understand the characteristics of the callsets. For this reason, I developed the R package acorn. Results: acorn is an R package that examines various features of de novo variants including subsetting the data by individual(s), variant type, or genomic region; calculating features including variant change counts, variant lengths, and presence/absence at CpG sites; and characteristics of parental age in relation to de novo variant counts. Conclusions: acorn is an R package that fills a critical gap in assessing de novo variants and will be of benefit to many investigators studying de novo variation.

Dysregulated cytokine and oxidative response in hyper-glycolytic monocytes in obesity

“…The subsequent analysis and related visualizations were performed in R-3.6.1 with the use of the packages limma ( 73 ), plyr ( 74 ), reshape2 ( 75 ), xlsx ( 76 ), DEP ( 77 ), calibrate ( 78 ), readxl ( 79 ), qpcR ( 80 ), splitstackshape ( 81 ), tidyr ( 82 ), Tmisc ( 83 ), ggplot2 ( 84 ), circlize ( 85 ), ggsci ( 86 ), dendsort ( 87 ), and dendextend ( 88 ).…”