EBSeq-HMM: a Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments

Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series

(2014) M. J. Nueda et al.   BIOINFORMATICS

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

(2014) Charity W Law et al.   GENOME BIOLOGY

EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments

(2013) Ning Leng et al.   BIOINFORMATICS

rSeqDiff: Detecting Differential Isoform Expression from RNA-Seq Data Using Hierarchical Likelihood Ratio Test

(2013) Yang Shi et al.   PLoS One

Identifying differentially expressed transcripts from RNA-seq data with biological variation

(2012) Peter Glaus et al.   BIOINFORMATICS

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Fast Computation and Applications of Genome Mappability

(2012) Thomas Derrien et al.   PLoS One

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Markov-switching autoregressive models for wind time series

(2011) Pierre Ailliot et al.   ENVIRONMENTAL MODELLING & SOFTWARE

The uniqueome: a mappability resource for short-tag sequencing

(2010) Ryan Koehler et al.   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

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

Anatomic Demarcation of Cells: Genes to Patterns

(2009) H. Y. Chang   SCIENCE

Regeneration, repair and remembering identity: the three Rs of Hox gene expression

(2009) Kevin C. Wang et al.   TRENDS IN CELL BIOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY