spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data

USP49 deubiquitinates histone H2B and regulates cotranscriptional pre-mRNA splicing

(2013) Z. Zhang et al.   GENES & DEVELOPMENT

CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model

(2013) Liguo Wang et al.   NUCLEIC ACIDS RESEARCH

SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts

(2012) Michael C. Ryan et al.   BIOINFORMATICS

MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data

(2012) Shihao Shen et al.   NUCLEIC ACIDS RESEARCH

The Evolutionary Landscape of Alternative Splicing in Vertebrate Species

(2012) N. L. Barbosa-Morais et al.   SCIENCE

Mammalian tissues defective in nonsense-mediated mRNA decay display highly aberrant splicing patterns

(2012) Joachim Weischenfeldt et al.   GENOME BIOLOGY

SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data

(2012) Mark F Rogers et al.   GENOME BIOLOGY

Detection, annotation and visualization of alternative splicing from RNA-Seq data with SplicingViewer

(2011) Qi Liu et al.   GENOMICS

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

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

(2010) Thomas J Hardcastle et al.   BMC BIOINFORMATICS

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

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