STAR: ultrafast universal RNA-seq aligner

Alexander Dobin, Carrie Davis, Felix Schlesinger, +6

Bioinformatics

WGCNA: an R package for weighted correlation network analysis

Peter Langfelder, Steve Horvath

BMC Bioinformatics

Comprehensive Integration of Single-Cell Data

Tim Stuart, Andrew Butler, Paul Hoffman, +7

Cell

EngineeringBiomedical Data IntegrationData ScienceSingle Cell SequencingMedicine +9

Integrated analysis of multimodal single-cell data

Yuhan Hao, Stephanie Hao, Erica Andersen‐Nissen, +22

Cell

Integrating single-cell transcriptomic data across different conditions, technologies, and species

Andrew Butler, Paul Hoffman, Peter Smibert, +2

Nature Biotechnology

EngineeringGeneticsMultiomicsSingle-cell Transcriptomic DataTranscriptomics Technology +15

Fast, sensitive and accurate integration of single-cell data with Harmony

Ilya Korsunsky, Nghia Millard, Jean Fan, +7

Nature Methods

BioinformaticsEngineeringData ScienceSingle Cell SequencingMedicine +12

Inference and analysis of cell-cell communication using CellChat

Suoqin Jin, Christian F. Guerrero‐Juarez, Lihua Zhang, +6

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

Dimensionality reduction for visualizing single-cell data using UMAP

Étienne Becht, Leland McInnes, John Healy, +5

Nature Biotechnology

Interactive VisualizationEngineeringData ScienceData VisualizationManagement +5

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

Paul J. McMurdie, Susan Holmes

PLoS Computational Biology

Microbial DiversityMicrobiome BiologyR PackageDysbiosisMolecular Ecology +12