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

Michael I. Love, Wolfgang Huber, Simon Anders

Genome biology

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

Ben Langmead, Cole Trapnell, Mihai Pop, +1

Genome biology

Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes

Jo Vandesompele, Katleen De Preter, Filip Pattyn, +4

Genome biology

Model-based Analysis of ChIP-Seq (MACS)

Yong Zhang, Tao Liu, Clifford A. Meyer, +8

Genome biology

Differential expression analysis for sequence count data

Simon Anders, Wolfgang Huber

Genome biology

EngineeringGenomicsGene Expression ProfilingHigh Throughput SequencingDifferential Expression Analysis +17

Metagenomic biomarker discovery and explanation

Nicola Segata, Jacques Izard, Levi Waldron, +4

Genome biology

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

Daehwan Kim, Geo Pertea, Cole Trapnell, +3

Genome biology

BioinformaticsGene Sequence AnnotationNatural SciencesGeneticsSequence Analysis +12

Bioconductor: open software development for computational biology and bioinformatics

Robert Gentleman, Vincent J. Carey, Douglas M. Bates, +22

Genome biology

DAVID: Database for Annotation, Visualization, and Integrated Discovery

Glynn Dennis, Brad T. Sherman, Douglas A Hosack, +4

Genome biology

SCANPY: large-scale single-cell gene expression data analysis

F. Alexander Wolf, Philipp Angerer, Fabian J. Theis

Genome biology