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Systematic transcriptome analysis allows the identification of new type I and type II Toxin/Antitoxin systems located in the superintegron of Vibrio cholerae.

Retrospective analysis of SARS-CoV-2 omicron invasion over delta in French regions in 2021-22: a status-based multi-variant model.

© Xavier Montagutelli, Institut Pasteur

Publication : G3 (Bethesda, Md.)

stuart: an R package for the curation of SNP genotypes from experimental crosses.

Team: Mouse Genetics

Member: Xavier Montagutelli

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Diseases

Organisms

Applications

Technique

Published in G3 (Bethesda, Md.) - 04 Nov 2022

Bourdon M, Montagutelli X

Link to Pubmed [PMID] – 36000885

Link to DOI – 10.1093/g3journal/jkac219

G3 (Bethesda) 2022 Nov; 12(11):

Genetic mapping in 2-generation crosses requires genotyping, usually performed with single nucleotide polymorphism markers arrays which provide high-density genetic information. However, genetic analysis on raw genotypes can lead to spurious or unreliable results due to defective single nucleotide polymorphism assays or wrong genotype interpretation. Here, we introduce stuart, an open-source R package, which analyzes raw genotyping data to filter single nucleotide polymorphism markers based on informativeness, Mendelian inheritance pattern, and consistency with parental genotypes. The functions of this package provide a curation pipeline and formatting adequate for genetic analysis with the R/qtl package. stuart is available with detailed documentation from https://gitlab.pasteur.fr/mouselab/stuart/.

Published on: 04 Nov 2022