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Longitudinal multi-omics analyses link gut microbiome dysbiosis with recurrent urinary tract infections in women

Colin J. Worby, Henry L. Schreiber, Timothy J. Straub, Lucas R. van Dijk, Ryan A. Bronson, Benjamin Olson, Jerome S. Pinkner, Chloe L. P. Obernuefemann, Vanessa L. Muñoz, Alexandra E. Paharik,

Nature Microbiology · 2022 · 178 citations · 47 references

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47

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Michael I. Love, Wolfgang Huber, Simon Anders · Genome biology · 2014 · 100.5K citations · Full text

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STAR: ultrafast universal RNA-seq aligner

Alexander Dobin, Carrie Davis, Felix Schlesinger et al. · Bioinformatics · 2012 · 56.2K citations · Full text

, , +17

<tt>edgeR</tt> : a Bioconductor package for differential expression analysis of digital gene expression data

Mark D. Robinson, Davis J. McCarthy, Gordon K. Smyth · Bioinformatics · 2009 · 44.5K citations · Full text

, , +14

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

Yang Liao, Gordon K. Smyth, Wei Shi · Bioinformatics · 2013 · 29.1K citations · Full text

, , +14

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

Anton Bankevich, Sergey Nurk, Dmitry Antipov et al. · Journal of Computational Biology · 2012 · 27.2K citations

, , +17