AS-Quant: Detection and Visualization of Alternative Splicing Events with RNA-seq Data

Deep-learning augmented RNA-seq analysis of transcript splicing

(2019) Zijun Zhang et al.   NATURE METHODS

mTOR-regulated U2af1 tandem exon splicing specifies transcriptome features for translational control

(2019) Jae-Woong Chang et al.   NUCLEIC ACIDS RESEARCH

Platform-integrated mRNA isoform quantification

(2019) Jiao Sun et al.   BIOINFORMATICS

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Network-Based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis

(2015) Wei Zhang et al.   PLoS Computational Biology

rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data

(2014) Shihao Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Splicing and alternative splicing in rice and humans

(2013) Zhiguo E et al.   BMB Reports

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Modelling and simulating generic RNA-Seq experiments with the flux simulator

(2012) Thasso Griebel et al.   NUCLEIC ACIDS RESEARCH

DiffSplice: the genome-wide detection of differential splicing events with RNA-seq

(2012) Yin Hu et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Shihao Shen et al.   NUCLEIC ACIDS RESEARCH

From RNA-seq reads to differential expression results

(2011) Alicia Oshlack et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS