Data-based RNA-seq simulations by binomial thinning

Droplet scRNA-seq is not zero-inflated

(2020) Valentine Svensson   NATURE BIOTECHNOLOGY

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

(2019) Tianyu Wang et al.   BMC BIOINFORMATICS

Accounting for unobserved covariates with varying degrees of estimability in high-dimensional biological data

(2019) Chris McKennan et al.   BIOMETRIKA

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

(2018) Zhun Miao et al.   BIOINFORMATICS

Empirical Bayes shrinkage and false discovery rate estimation, allowing for unwanted variation

(2018) David Gerard et al.   BIOSTATISTICS

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

(2018) Tianyu Wang et al.   METHODS

A general and flexible method for signal extraction from single-cell RNA-seq data

(2018) Davide Risso et al.   Nature Communications

A robust RUV-testing procedure via γ-divergence

(2018) Hung Hung   BIOMETRICS

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

Single-cell mRNA quantification and differential analysis with Census

(2017) Xiaojie Qiu et al.   NATURE METHODS

Massively parallel digital transcriptional profiling of single cells

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

Controlling for Confounding Effects in Single Cell RNA Sequencing Studies Using both Control and Target Genes

(2017) Mengjie Chen et al.   Scientific Reports

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

(2016) Mihails Delmans et al.   BMC BIOINFORMATICS

Statistical evaluation of methods for identification of differentially abundant genes in comparative metagenomics

(2016) Viktor Jonsson et al.   BMC GENOMICS

Order-invariant prior specification in Bayesian factor analysis

(2016) Dennis Leung et al.   STATISTICS & PROBABILITY LETTERS

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

(2015) Sheida Nabavi et al.   BIOINFORMATICS

SimSeq: a nonparametric approach to simulation of RNA-sequence datasets

(2015) Sam Benidt et al.   BIOINFORMATICS

Evaluation of methods for differential expression analysis on multi-group RNA-seq count data

(2015) Min Tang et al.   BMC BIOINFORMATICS

Computational assignment of cell-cycle stage from single-cell transcriptome data

(2015) Antonio Scialdone et al.   METHODS

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

subSeq: Determining Appropriate Sequencing Depth Through Efficient Read Subsampling

(2014) David G. Robinson et al.   BIOINFORMATICS

ShrinkBayes: a versatile R-package for analysis of count-based sequencing data in complex study designs

(2014) Mark A van de Wiel et al.   BMC BIOINFORMATICS

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

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

Bayesian approach to single-cell differential expression analysis

(2014) Peter V Kharchenko et al.   NATURE METHODS

svaseq: removing batch effects and other unwanted noise from sequencing data

(2014) Jeffrey T. Leek   NUCLEIC ACIDS RESEARCH

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

(2014) Charity W Law et al.   GENOME BIOLOGY

Sparse latent factor models with interactions: Analysis of gene expression data

(2013) Vinicius Diniz Mayrink et al.   Annals of Applied Statistics

Accounting for non-genetic factors by low-rank representation and sparse regression for eQTL mapping

(2013) Can Yang et al.   BIOINFORMATICS

A Sparse Singular Value Decomposition Method for High-Dimensional Data

(2013) Dan Yang et al.   JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS

Normalizing RNA-Sequencing Data by Modeling Hidden Covariates with Prior Knowledge

(2013) Sara Mostafavi et al.   PLoS One

Evaluating statistical analysis models for RNA sequencing experiments

(2013) Pablo D. Reeb et al.   Frontiers in Genetics

A comparison of statistical methods for detecting differentially expressed genes from RNA-seq data

(2012) Vanessa M. Kvam et al.   AMERICAN JOURNAL OF BOTANY

Multiple hypothesis testing adjusted for latent variables, with an application to the AGEMAP gene expression data

(2012) Yunting Sun et al.   Annals of Applied Statistics

Bayesian analysis of RNA sequencing data by estimating multiple shrinkage priors

(2012) M. A. Van De Wiel et al.   BIOSTATISTICS

A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis

(2012) M.-A. Dillies et al.   BRIEFINGS IN BIOINFORMATICS

Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses

(2012) Oliver Stegle et al.   Nature Protocols

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

Using control genes to correct for unwanted variation in microarray data

(2011) J. A. Gagnon-Bartsch et al.   BIOSTATISTICS

GC-Content Normalization for RNA-Seq Data

(2011) Davide Risso et al.   BMC BIOINFORMATICS

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

(2010) James H Bullard et al.   BMC BIOINFORMATICS

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

(2010) Thomas J Hardcastle et al.   BMC BIOINFORMATICS

Subset Quantile Normalization Using Negative Control Features

(2010) Zhijin Wu et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A Factor Model Approach to Multiple Testing Under Dependence

(2010) Chloé Friguet et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Variance component model to account for sample structure in genome-wide association studies

(2010) Hyun Min Kang et al.   NATURE GENETICS

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

Correction for hidden confounders in the genetic analysis of gene expression

(2010) J. Listgarten et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cloud-scale RNA-sequencing differential expression analysis with Myrna

(2010) Ben Langmead et al.   GENOME BIOLOGY

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

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

A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis

(2009) D. M. Witten et al.   BIOSTATISTICS

Default Prior Distributions and Efficient Posterior Computation in Bayesian Factor Analysis

(2009) Joyee Ghosh et al.   JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS

High-Dimensional Sparse Factor Modeling: Applications in Gene Expression Genomics

(2009) Carlos M. Carvalho et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Bayes factors for genome-wide association studies: comparison withP-values

(2008) Jon Wakefield   GENETIC EPIDEMIOLOGY

Accurate Discovery of Expression Quantitative Trait Loci Under Confounding From Spurious and Genuine Regulatory Hotspots

(2008) H. M. Kang et al.   GENETICS

Efficient Control of Population Structure in Model Organism Association Mapping

(2008) H. M. Kang et al.   GENETICS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

A general framework for multiple testing dependence

(2008) J. T. Leek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA