Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data

DEsingle for detecting three types of differential expression in single-cell RNA-seq data

(2018) Zhun Miao et al.   BIOINFORMATICS

SigEMD: A powerful method for differential gene expression analysis in single-cell RNA sequencing data

(2018) Tianyu Wang et al.   METHODS

Single-cell mRNA quantification and differential analysis with Census

(2017) Xiaojie Qiu et al.   NATURE METHODS

Single-Cell RNA-Sequencing: Assessment of Differential Expression Analysis Methods

(2017) Alessandra Dal Molin et al.   Frontiers in Genetics

Analysis of aggregated cell–cell statistical distances within pathways unveils therapeutic-resistance mechanisms in circulating tumor cells

(2016) A. Grant Schissler et al.   BIOINFORMATICS

Discrete distributional differential expression (D3E) - a tool for gene expression analysis of single-cell RNA-seq data

(2016) Mihails Delmans et al.   BMC BIOINFORMATICS

Comparison of methods to detect differentially expressed genes between single-cell populations

(2016) Maria K. Jaakkola et al.   BRIEFINGS IN BIOINFORMATICS

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

(2016) I. Tirosh et al.   SCIENCE

EMDomics: a robust and powerful method for the identification of genes differentially expressed between heterogeneous classes

(2015) Sheida Nabavi et al.   BIOINFORMATICS

Design and Analysis of Single-Cell Sequencing Experiments

(2015) Dominic Grün et al.   CELL

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

A survey of human brain transcriptome diversity at the single cell level

(2015) Spyros Darmanis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2015) Minzhe Guo et al.   PLoS Computational Biology

Differentially Expressed Genes and Signature Pathways of Human Prostate Cancer

(2015) Jennifer S. Myers et al.   PLoS One

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

(2014) Cole Trapnell 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

Single-cell RNA-seq: advances and future challenges

(2014) Antoine-Emmanuel Saliba et al.   NUCLEIC ACIDS RESEARCH

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

(2014) A. P. Patel et al.   SCIENCE

SAMstrt: statistical test for differential expression in single-cell transcriptome with spike-in normalization

(2013) Shintaro Katayama et al.   BIOINFORMATICS

EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments

(2013) Ning Leng et al.   BIOINFORMATICS

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

(2013) C. D. Arnold et al.   SCIENCE

High-Throughput Single-Cell Manipulation in Brain Tissue

(2012) Joseph D. Steinmeyer et al.   PLoS One

Comparative RNA sequencing reveals substantial genetic variation in endangered primates

(2011) G. H. Perry et al.   GENOME RESEARCH

Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq

(2011) S. Islam et al.   GENOME RESEARCH

Differential expression in RNA-seq: A matter of depth

(2011) S. Tarazona et al.   GENOME RESEARCH

The NBP Negative Binomial Model for Assessing Differential Gene Expression from RNA-Seq

(2011) Yanming Di et al.   Statistical Applications in Genetics and Molecular Biology

A Two-Stage Poisson Model for Testing RNA-Seq Data

(2011) Paul L. Auer et al.   Statistical Applications in Genetics and Molecular Biology

Finding consistent patterns: A nonparametric approach for identifying differential expression in RNA-Seq data

(2011) Jun Li et al.   STATISTICAL METHODS IN MEDICAL RESEARCH

baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data

(2010) Thomas J Hardcastle et al.   BMC BIOINFORMATICS

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

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

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

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences

(2008) Arjun Raj et al.   CELL

Mouse Embryonic Stem Cell-Derived Spheres with Distinct Neurogenic Potentials

(2008) Annalena Moliner et al.   STEM CELLS AND DEVELOPMENT