3D RNA-seq: a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists

Cold-Dependent Expression and Alternative Splicing of Arabidopsis Long Non-coding RNAs

(2019) Cristiane P. G. Calixto et al.   Frontiers in Plant Science

RNA-Seq transcriptome analysis shows anti-tumor actions of melatonin in a breast cancer xenograft model

(2019) Bruna Victorasso Jardim-Perassi et al.   Scientific Reports

Time-Course Transcriptome Analysis for Drug Repositioning in Fusobacterium nucleatum-Infected Human Gingival Fibroblasts

(2019) Wenyan Kang et al.   Frontiers in Cell and Developmental Biology

A comparison of the sexually dimorphic dexamethasone transcriptome in mouse cerebral cortical and hypothalamic embryonic neural stem cells

(2018) Krystle A. Frahm et al.   MOLECULAR AND CELLULAR ENDOCRINOLOGY

Rapid and dynamic alternative splicing impacts the Arabidopsis cold response transcriptome

(2018) Cristiane P G Calixto et al.   PLANT CELL

Differential analysis of RNA-seq incorporating quantification uncertainty

(2017) Harold Pimentel et al.   NATURE METHODS

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing

(2017) Runxuan Zhang et al.   NUCLEIC ACIDS RESEARCH

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Evaluation of methods for differential expression analysis on multi-group RNA-seq count data

(2015) Min Tang et al.   BMC BIOINFORMATICS

RNA-Seq analysis of the wild barley (H. spontaneum) leaf transcriptome under salt stress

(2015) Ahmed Bahieldin et al.   COMPTES RENDUS BIOLOGIES

AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression inArabidopsis thaliana

(2015) Runxuan Zhang et al.   NEW PHYTOLOGIST

Detection of recurrent alternative splicing switches in tumor samples reveals novel signatures of cancer

(2015) Endre Sebestyén et al.   NUCLEIC ACIDS RESEARCH

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Why weight? Modelling sample and observational level variability improves power in RNA-seq analyses

(2015) Ruijie Liu et al.   NUCLEIC ACIDS RESEARCH

Leveraging transcript quantification for fast computation of alternative splicing profiles

(2015) Gael P. Alamancos et al.   RNA

Normalization of RNA-seq data using factor analysis of control genes or samples

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

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

(2014) Charity W Law et al.   GENOME BIOLOGY

The analytical landscape of static and temporal dynamics in transcriptome data

(2014) Sunghee Oh et al.   Frontiers in Genetics

RDAVIDWebService: a versatile R interface to DAVID

(2013) C. Fresno et al.   BIOINFORMATICS

Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

(2013) Franck Rapaport et al.   GENOME BIOLOGY

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

(2010) James H Bullard 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

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS