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
Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data
Paulson J, Chen C, Lopes-Ramos C, Kuijjer M, Platig J, Sonawane A, Fagny M, Glass K, Quackenbush J. Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data. BMC Bioinformatics 2017, 18: 437. PMID: 28974199, PMCID: PMC5627434, DOI: 10.1186/s12859-017-1847-x.Peer-Reviewed Original ResearchConceptsRNA-seq data setsRNA-seqGenotype-Tissue ExpressionRNA-seq processingGenome-wide transcriptional profilingRNA-seq studiesRNA-seq dataGene filteringDownstream analysisRNA sequencingTranscriptional profilesDiverse tissuesAnalytical pipelineR packageQuality controlSignificant analytical challengeSoftware pipelineGenesRNAMulti-group studyNormalization stepAnalytical challengesResultsWeTissueExpression