2023
mbQTL: an R/Bioconductor package for microbial quantitative trait loci (QTL) estimation
Movassagh M, Schiff S, Paulson J. mbQTL: an R/Bioconductor package for microbial quantitative trait loci (QTL) estimation. Bioinformatics 2023, 39: btad565. PMID: 37707523, PMCID: PMC10516520, DOI: 10.1093/bioinformatics/btad565.Peer-Reviewed Original ResearchConceptsSingle nucleotide variationsRNA sequencingMicrobial abundance dataQuantitative trait lociSingle nucleotide polymorphism dataRibosomal RNA sequencingField of genomicsWhole-genome sequencingEvidence of interplayMutational profileTrait lociMicrobial communitiesMicrobial abundancePolymorphism dataMicrobial populationsGenome sequencingAbundance dataFirst R packageHuman geneticsBioconductor packageGenetic variantsMicrobiome dataSequencingR packageAbundance
2017
Smooth quantile normalization
Hicks S, Okrah K, Paulson J, Quackenbush J, Irizarry R, Bravo H. Smooth quantile normalization. Biostatistics 2017, 19: 185-198. PMID: 29036413, PMCID: PMC5862355, DOI: 10.1093/biostatistics/kxx028.Peer-Reviewed Original ResearchConceptsMonte Carlo simulation studyGlobal normalization methodsQuantile normalizationBias-variance tradeoffSimulation studyHigh-throughput datasetsSequencing read countsHigh-throughput dataGenomic data analysisSmooth quantile normalizationTechnical variationBetween-sample normalizationBiological conditionsGlobal propertiesStatistical distributionBiological groupsNormalizationReducing other formsGlobal differences