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

Michael I. Love, Wolfgang Huber, Simon Anders

Genome biology

STAR: ultrafast universal RNA-seq aligner

Alexander Dobin, Carrie Davis, Felix Schlesinger, +6

Bioinformatics

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

Guangchuang Yu, Li-Gen Wang, Yanyan Han, +1

OMICS A Journal of Integrative Biology

GeneticsGenomicsGene RecognitionBioinformatics DatabaseR Package +22

Visualizing Data using t-SNE

Laurens van der Maaten, Geoffrey E. Hinton

Journal of Machine Learning Research

EngineeringData VisualizationData ExplorationVisualization (Data Visualization)Linear Embedding +14

Salmon provides fast and bias-aware quantification of transcript expression

Rob Patro, Geet Duggal, Michael I. Love, +2

Nature Methods

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

Evan Z. Macosko, Anindita Basu, Rahul Satija, +12

Cell

Systems BiologyFunctional GenomicsSingle Cell SequencingMedicineNatural Sciences +10

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

Spatial reconstruction of single-cell gene expression data

Rahul Satija, Jeffrey A. Farrell, David Gennert, +2

Nature Biotechnology

Functional GenomicsEngineeringSingle Cell SequencingMedicineSpatial Omics +8

SCENIC: single-cell regulatory network inference and clustering

Sara Aibar, Carmen Bravo González‐Blas, Thomas Moerman, +11

Nature Methods

Functional GenomicsEngineeringMedicineBiological NetworkComputational Biology +7

Dimensionality reduction for visualizing single-cell data using UMAP

Étienne Becht, Leland McInnes, John Healy, +5

Nature Biotechnology

Interactive VisualizationEngineeringData ScienceData VisualizationManagement +5