Cited in
(91)- methylGSA
- Modeling overdispersion heterogeneity in differential expression analysis using mixtures
- Poisson–Tweedie mixed-effects model: A flexible approach for the analysis of longitudinal RNA-seq data
- A model selection criterion for model-based clustering of annotated gene expression data
- Yanagi: transcript segment library construction for RNA-seq quantification
- An empirical Bayes change-point model for transcriptome time-course data
- A semi-parametric Bayesian approach for differential expression analysis of RNA-seq data
- RCRnorm: an integrated system of random-coefficient hierarchical regression models for normalizing nanostring nCounter data
- Analysis of expression profile and gene variation via development of methods for next generation sequencing data
- Pathway analysis for RNA-seq data using a score-based approach
- A statistical perspective on the challenges in molecular microbial biology
- No counts, no variance: allowing for loss of degrees of freedom when assessing biological variability from RNA-seq data
- Detecting differentially expressed genes with RNA-seq data using backward selection to account for the effects of relevant covariates
- Hierarchical modeling and differential expression analysis for RNA-seq experiments with inbred and hybrid genotypes
- Modeling microbial abundances and dysbiosis with beta-binomial regression
- SummarizedExperiment
- ICeD-t provides accurate estimates of immune cell abundance in tumor samples by allowing for aberrant gene expression patterns
- STAR
- Bioconductor
- gcrma
- edgeR
- SAM
- DEGseq
- ARSyN
- BaySeq
- DEseq
- limma
- RUVseq
- maSigPro
- QuasiSeq
- ClustOfVar
- Phyloseq
- ShrinkBayes
- svaseq
- DOTUR
- propr
- DOSE
- HTSeq
- DiffSplice
- DoubleExpSeq
- featureCounts
- NBC
- recount
- Rsubread
- TopHat
- qvalue
- csaw
- Scotty
- diffHic
- compcodeR
- DEXUS
- GSNCA
- goseq
- GSAASeqSP
- sydSeq
- betapart
- MDSINE
- NeatMap
- UrQt
- rSeqDiff
- clusterProfiler
- GlobalAncova
- CAMERA
- SpliceTrap
- calm
- Salmon
- iBAG
- NanoStringNorm
- gfpop
- topGO
- DivNet
- RapMap
- UPARSE
- USEARCH
- Yanagi
- SimSeq
- PePr
- sansSouci
- lemma
- PLNseq
- ggbio
- MAnorm
- ACAT
- DESMAN
- Robust hyperparameter estimation protects against hypervariable genes and improves power to detect differential expression
- Shrinkage of dispersion parameters in the binomial family, with application to differential exon skipping
- Statistical analysis of microbiome data with R
- DESeq2
- glmGamPoi
- Empirical Bayes analysis of RNA sequencing experiments with auxiliary information
- ptmixed
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