ArticleBMC bioinformatics2023
Acorn: an R package for de novo variant analysis.
Article in BMC bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
3 citing papers in PubMed.
- Sex-aware genome-wide assessment of de novo variants in autism across coding and noncoding regions.Human genomics · 2026Article
- De Novo Variation in Autism by Sex and Diagnostic Status in 41,367 Parent-Child Trios.medRxiv : the preprint server for health sciences · 2026Article
- Whole-genome sequencing reveals individual and cohort level insights into chromosome 9p syndromes.Genome medicine · 2025Article
Corrections and comments
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Authors and funding
1 author.
Funding
Abstract
backgroundThe 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 an R package called acorn.
resultsAcorn 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.
conclusionsAcorn 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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.