lmerSeq: an R package for analyzing transformed RNA-Seq data with linear mixed effects models

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

(2022) Elizabeth A. Wynn et al.   BMC Medical Research Methodology

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

(2020) Yet Nguyen et al.   BIOINFORMATICS

dream: Powerful differential expression analysis for repeated measures designs

(2020) Gabriel E Hoffman et al.   BIOINFORMATICS

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

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

Increased biological relevance of transcriptome analyses in human skeletal muscle using a model-specific pipeline

(2020) Yusuf Khan 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

Balancing Type I error and power in linear mixed models

(2017) Hannes Matuschek et al.   JOURNAL OF MEMORY AND LANGUAGE

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

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

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

Random effects structure for confirmatory hypothesis testing: Keep it maximal

(2013) Dale J. Barr et al.   JOURNAL OF MEMORY AND LANGUAGE

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

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