PIVOT: platform for interactive analysis and visualization of transcriptomics data

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

Michael I. Love, Wolfgang Huber, Simon Anders · Genome biology · 2014 · 94.7K citations · Full text

Visualizing Data using t-SNE

Laurens van der Maaten, Geoffrey E. Hinton · Journal of Machine Learning Research · 2008 · 35.7K citations

Engineering, Data Visualization, Data Exploration +16

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

Yang Liao, Gordon K. Smyth, Wei Shi · Bioinformatics · 2013 · 27.4K citations · Full text

HTSeq—a Python framework to work with high-throughput sequencing data

Simon Anders, Paul Theodor Pyl, Wolfgang Huber · Bioinformatics · 2014 · 21.9K citations · Full text

Differential expression analysis for sequence count data

Simon Anders, Wolfgang Huber · Genome biology · 2010 · 16.1K citations · Full text

Engineering, Genomics, Gene Expression Profiling +19