Metacells untangle large and complex single-cell transcriptome networks

COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas

(2021) Xianwen Ren et al.   CELL

A pan-cancer single-cell transcriptional atlas of tumor infiltrating myeloid cells

(2021) Sijin Cheng et al.   CELL

Linear-time cluster ensembles of large-scale single-cell RNA-seq and multimodal data

(2021) Van Hoan Do et al.   GENOME RESEARCH

Identification of resistance pathways and therapeutic targets in relapsed multiple myeloma patients through single-cell sequencing

(2021) Yael C. Cohen et al.   NATURE MEDICINE

Ultra-high-throughput single-cell RNA sequencing and perturbation screening with combinatorial fluidic indexing

(2021) Paul Datlinger et al.   NATURE METHODS

Confronting false discoveries in single-cell differential expression

(2021) Jordan W. Squair et al.   Nature Communications

TooManyCells identifies and visualizes relationships of single-cell clades

(2020) Gregory W. Schwartz et al.   NATURE METHODS

A cell atlas of human thymic development defines T cell repertoire formation

(2020) Jong-Eun Park et al.   SCIENCE

Host-Viral Infection Maps Reveal Signatures of Severe COVID-19 Patients

(2020) Pierre Bost et al.   CELL

Single-cell analysis of clonal maintenance of transcriptional and epigenetic states in cancer cells

(2020) Zohar Meir et al.   NATURE GENETICS

Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis

(2020) Taylor S. Adams et al.   Science Advances

NeuralEE: A GPU-Accelerated Elastic Embedding Dimensionality Reduction Method for Visualizing Large-Scale scRNA-Seq Data

(2020) Jiankang Xiong et al.   Frontiers in Genetics

Tumor-infiltrating dendritic cell states are conserved across solid human cancers

(2020) Genevieve M. Gerhard et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Single-Cell Transcriptomics of Human and Mouse Lung Cancers Reveals Conserved Myeloid Populations across Individuals and Species

(2019) Rapolas Zilionis et al.   IMMUNITY

Efficient integration of heterogeneous single-cell transcriptomes using Scanorama

(2019) Brian Hie et al.   NATURE BIOTECHNOLOGY

Benchmarking single cell RNA-sequencing analysis pipelines using mixture control experiments

(2019) Luyi Tian et al.   NATURE METHODS

Comprehensive single cell mRNA profiling reveals a detailed roadmap for pancreatic endocrinogenesis

(2019) Aimée Bastidas-Ponce et al.   DEVELOPMENT

Current best practices in single‐cell RNA‐seq analysis: a tutorial

(2019) Malte D Luecken et al.   Molecular Systems Biology

Geometric Sketching Compactly Summarizes the Single-Cell Transcriptomic Landscape

(2019) Brian Hie et al.   Cell Systems

SSCC: A Novel Computational Framework for Rapid and Accurate Clustering Large-scale Single Cell RNA-seq Data

(2019) Xianwen Ren et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

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

(2019) Ilya Korsunsky et al.   NATURE METHODS

Orchestrating single-cell analysis with Bioconductor

(2019) Robert A. Amezquita et al.   NATURE METHODS

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

(2018) David van Dijk et al.   CELL

Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment

(2018) Elham Azizi et al.   CELL

bigSCale: an analytical framework for big-scale single-cell data

(2018) Giovanni Iacono et al.   GENOME RESEARCH

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Conserved properties of dentate gyrus neurogenesis across postnatal development revealed by single-cell RNA sequencing

(2018) Hannah Hochgerner et al.   NATURE NEUROSCIENCE

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

A test metric for assessing single-cell RNA-seq batch correction

(2018) Maren Büttner et al.   NATURE METHODS

Comparative Analysis of Single-Cell RNA Sequencing Methods

(2017) Christoph Ziegenhain et al.   MOLECULAR CELL

SC3: consensus clustering of single-cell RNA-seq data

(2017) Vladimir Yu Kiselev et al.   NATURE METHODS

In situ click chemistry generation of cyclooxygenase-2 inhibitors

(2017) Atul Bhardwaj et al.   Nature Communications

Immunogenic Chemotherapy Sensitizes Tumors to Checkpoint Blockade Therapy

(2016) Christina Pfirschke et al.   IMMUNITY

RNA-seq mixology: designing realistic control experiments to compare protocols and analysis methods

(2016) Aliaksei Z. Holik et al.   NUCLEIC ACIDS RESEARCH

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

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

(2015) Evan Z. Macosko et al.   CELL

Single-cell messenger RNA sequencing reveals rare intestinal cell types

(2015) Dominic Grün et al.   NATURE

Copy Number Loss of the Interferon Gene Cluster in Melanomas Is Linked to Reduced T Cell Infiltrate and Poor Patient Prognosis

(2014) Peter S. Linsley et al.   PLoS One

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS