A comparison of methods for multiple degree of freedom testing in repeated measures RNA-sequencing experiments

A practical solution to pseudoreplication bias in single-cell studies

(2021) Kip D. Zimmerman et al.   Nature Communications

rmRNAseq: Differential Expression Analysis for Repeated-measures RNA-seq Data

(2020) Yet Nguyen et al.   BIOINFORMATICS

MCMSeq: Bayesian hierarchical modeling of clustered and repeated measures RNA sequencing experiments

(2020) Brian E. Vestal et al.   BMC BIOINFORMATICS

A modular transcriptional signature identifies phenotypic heterogeneity of human tuberculosis infection

(2018) Akul Singhania et al.   Nature Communications

PairedFB: a full hierarchical Bayesian model for paired RNA-seq data with heterogeneous treatment effects

(2018) Yuanyuan Bian et al.   BIOINFORMATICS

Longitudinal transcriptomic characterization of the immune response to acute hepatitis C virus infection in patients with spontaneous viral clearance

(2018) Brad R. Rosenberg et al.   PLoS Pathogens

Negative Binomial Mixed Models for Analyzing Longitudinal Microbiome Data

(2018) Xinyan Zhang et al.   Frontiers in Microbiology

lmerTest Package: Tests in Linear Mixed Effects Models

(2017) Alexandra Kuznetsova et al.   Journal of Statistical Software

multiDE: a dimension reduced model based statistical method for differential expression analysis using RNA-sequencing data with multiple treatment conditions

(2016) Guangliang Kang et al.   BMC BIOINFORMATICS

What if we ignore the random effects when analyzing RNA-seq data in a multifactor experiment

(2016) Shiqi Cui et al.   Statistical Applications in Genetics and Molecular Biology

What if we ignore the random effects when analyzing RNA-seq data in a multifactor experiment

(2016) Shiqi Cui et al.   Statistical Applications in Genetics and Molecular Biology

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

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

PLNseq: a multivariate Poisson lognormal distribution for high-throughput matched RNA-sequencing read count data

(2015) Hong Zhang et al.   STATISTICS IN MEDICINE

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

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

(2014) Charity W Law et al.   GENOME BIOLOGY

Empirical Bayesian analysis of paired high-throughput sequencing data with a beta-binomial distribution

(2013) Thomas J Hardcastle et al.   BMC BIOINFORMATICS

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

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

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

AD Model Builder: using automatic differentiation for statistical inference of highly parameterized complex nonlinear models

(2011) David A. Fournier et al.   OPTIMIZATION METHODS & SOFTWARE

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

(2010) Thomas J Hardcastle et al.   BMC BIOINFORMATICS

Modified robust variance estimator for generalized estimating equations with improved small-sample performance

(2010) Ming Wang et al.   STATISTICS IN MEDICINE

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