An interpretable framework for clustering single-cell RNA-Seq datasets

Assembly of functionally integrated human forebrain spheroids

(2017) Fikri Birey et al.   NATURE

Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning

(2017) Bo Wang et al.   NATURE METHODS

Single-cell mRNA quantification and differential analysis with Census

(2017) Xiaojie Qiu et al.   NATURE METHODS

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

(2017) Vladimir Yu Kiselev et al.   NATURE METHODS

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

OEFinder: a user interface to identify and visualize ordering effects in single-cell RNA-seq data

(2016) Ning Leng et al.   BIOINFORMATICS

pcaReduce: hierarchical clustering of single cell transcriptional profiles

(2016) Justina žurauskienė et al.   BMC BIOINFORMATICS

Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis

(2016) Jean Fan et al.   NATURE METHODS

Identification of cell types from single-cell transcriptomes using a novel clustering method

(2015) Chen Xu et al.   BIOINFORMATICS

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

(2015) Evan Z. Macosko et al.   CELL

Defining cell types and states with single-cell genomics

(2015) Cole Trapnell   GENOME RESEARCH

Single-cell messenger RNA sequencing reveals rare intestinal cell types

(2015) Dominic Grün et al.   NATURE

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

(2015) Florian Buettner et al.   NATURE BIOTECHNOLOGY

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Combinatorial labeling of single cells for gene expression cytometry

(2015) H. C. Fan et al.   SCIENCE

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data

(2015) Catalina A. Vallejos et al.   PLoS Computational Biology

SINCERA: A Pipeline for Single-Cell RNA-Seq Profiling Analysis

(2015) Minzhe Guo et al.   PLoS Computational Biology

Cell fate inclination within 2-cell and 4-cell mouse embryos revealed by single-cell RNA sequencing

(2014) Fernando H. Biase et al.   GENOME RESEARCH

Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq

(2014) Barbara Treutlein et al.   NATURE

Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex

(2014) Alex A Pollen et al.   NATURE BIOTECHNOLOGY

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Normalization of RNA-seq data using factor analysis of control genes or samples

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

Validation of noise models for single-cell transcriptomics

(2014) Dominic Grün et al.   NATURE METHODS

Bayesian approach to single-cell differential expression analysis

(2014) Peter V Kharchenko et al.   NATURE METHODS

Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing

(2014) Dmitry Usoskin et al.   NATURE NEUROSCIENCE

Accounting for technical noise in single-cell RNA-seq experiments

(2013) Philip Brennecke et al.   NATURE METHODS

Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells

(2013) Liying Yan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

(2012) Jeffrey T. Leek et al.   BIOINFORMATICS

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

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