STAR: ultrafast universal RNA-seq aligner

Alexander Dobin, Carrie Davis, Felix Schlesinger, +6

Bioinformatics

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

Simon Anders, Paul Theodor Pyl, Wolfgang Huber

Bioinformatics

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

Maxim V. Kuleshov, Matthew R. Jones, Andrew D. Rouillard, +11

Nucleic Acids Research

GeneticsMolecular BiologyCurated Gene SetsGenomicsGene Recognition +18

UMAP: Uniform Manifold Approximation and Projection

Leland McInnes, John Healy, Nathaniel Saul, +1

The Journal of Open Source Software

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

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

Genome biology

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

Cole Trapnell, Davide Cacchiarelli, Jonna Grimsby, +7

Nature Biotechnology

Pattern FormationDevelopmental BiologyCell DivisionCell InteractionSingle-cell Biology +10

Massively parallel digital transcriptional profiling of single cells

Grace Zheng, Jessica M. Terry, Phillip Belgrader, +30

Nature Communications

UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction

Leland McInnes, John J. Healy

Deep Blue (University of Michigan)

Geometric ModelingEngineeringMachine LearningData ScienceData Mining +13

NOTES ON CONTINUOUS STOCHASTIC PHENOMENA

P. A. P. Moran

Biometrika

Large DeviationsEngineeringOxford University SearchStochastic AnalysisStochastic Phenomenon +14

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

Jason D. Buenrostro, Paul G. Giresi, Lisa C. Zaba, +2

Nature Methods

ChromatinNative ChromatinChromatin RemodelingNatural SciencesGenetics +13