clusterExperiment and RSEC: A Bioconductor package and framework for clustering of single-cell and other large gene expression datasets

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

(2018) Kelly Street et al.   BMC GENOMICS

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

(2017) Vladimir Yu Kiselev et al.   NATURE METHODS

Single-Cell RNA-Seq Reveals Hypothalamic Cell Diversity

(2017) Renchao Chen et al.   Cell Reports

pcaReduce: hierarchical clustering of single cell transcriptional profiles

(2016) Justina žurauskienė et al.   BMC BIOINFORMATICS

TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis

(2016) Zhicheng Ji et al.   NUCLEIC ACIDS RESEARCH

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

Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis

(2015) Jaehoon Shin et al.   Cell Stem Cell

Single-cell messenger RNA sequencing reveals rare intestinal cell types

(2015) Dominic Grün et al.   NATURE

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

(2015) Minzhe Guo et al.   PLoS Computational Biology

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

Effects of resampling method and adaptation on clustering ensemble efficacy

(2011) Behrouz Minaei-Bidgoli et al.   ARTIFICIAL INTELLIGENCE REVIEW

Bagging-based spectral clustering ensemble selection

(2011) Jianhua Jia et al.   PATTERN RECOGNITION LETTERS

ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking

(2010) Matthew D. Wilkerson et al.   BIOINFORMATICS

A flexible R package for nonnegative matrix factorization

(2010) Renaud Gaujoux et al.   BMC BIOINFORMATICS

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

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