DESeq2

swMATH41938MaRDI QIDQ1353038FDOQ1353038

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Source code repository: https://github.com/mikelove/DESeq2

Cited In (26)

• An empirical Bayes change-point model for transcriptome time-course data
• Improved outcome prediction across data sources through robust parameter tuning
• Optimal false discovery rate control for large scale multiple testing with auxiliary information
• BNP-Seq: Bayesian Nonparametric Differential Expression Analysis of Sequencing Count Data
• Exponential-Family Embedding With Application to Cell Developmental Trajectories for Single-Cell RNA-Seq Data
• Rejoinder for “Exponential-Family Embedding With Application to Cell Developmental Trajectories for Single-Cell RNA-Seq Data”
• Poisson–Tweedie mixed-effects model: A flexible approach for the analysis of longitudinal RNA-seq data
• Empirical likelihood tests for nonparametric detection of differential expression from RNA-seq data
• Model-based feature selection and clustering of RNA-seq data for unsupervised subtype discovery
• Interactive Visualization of Hierarchically Structured Data
• Discrimination of attractors with noisy nodes in Boolean networks
• Modifying SAMseq to account for asymmetry in the distribution of effect sizes when identifying differentially expressed genes
• A compositional model to assess expression changes from single-cell RNA-seq data
• Modeling overdispersion heterogeneity in differential expression analysis using mixtures
• Hierarchical modeling and differential expression analysis for RNA-seq experiments with inbred and hybrid genotypes
• \texttt{TopKLists}: a comprehensive \texttt{R} package for statistical inference, stochastic aggregation, and visualization of multiple omics ranked lists
• Bayesian analysis of RNA-Seq data using a family of negative binomial models
• Modeling microbial abundances and dysbiosis with beta-binomial regression
• Maximum Rank Reproducibility: A Nonparametric Approach to Assessing Reproducibility in Replicate Experiments
• Estimating cellular redundancy in networks of genetic expression
• Zero-inflated quantile rank-score based test (ZIQRank) with application to scRNA-seq differential gene expression analysis
• \texttt{EBADIMEX}: an empirical Bayes approach to detect joint differential expression and methylation and to classify samples
• Model-based approach to the joint analysis of single-cell data on chromatin accessibility and gene expression
• Symmetric directional false discovery rate control
• Adaptive gPCA: a method for structured dimensionality reduction with applications to microbiome data
• Tuning parameter selection for a penalized estimator of species richness

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