CLASS2: accurate and efficient splice variant annotation from RNA-seq reads
Next generation sequencing of cellular RNA is making it possible to characterize genes and
alternative splicing in unprecedented detail. However, designing bioinformatics tools to …
alternative splicing in unprecedented detail. However, designing bioinformatics tools to …
SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts
MC Ryan, J Cleland, RG Kim, WC Wong… - …, 2012 - academic.oup.com
SpliceSeq is a resource for RNA-Seq data that provides a clear view of alternative splicing
and identifies potential functional changes that result from splice variation. It displays …
and identifies potential functional changes that result from splice variation. It displays …
ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events
Background While the reconstruction of transcripts from a sample of RNA-Seq data is a
computationally expensive and complicated task, the detection of splicing events from RNA …
computationally expensive and complicated task, the detection of splicing events from RNA …
Prediction and quantification of splice events from RNA-seq data
LD Goldstein, Y Cao, G Pau, M Lawrence, TD Wu… - PloS one, 2016 - journals.plos.org
Analysis of splice variants from short read RNA-seq data remains a challenging problem.
Here we present a novel method for the genome-guided prediction and quantification of …
Here we present a novel method for the genome-guided prediction and quantification of …
MAJIQ-SPEL: web-tool to interrogate classical and complex splicing variations from RNA-Seq data
CJ Green, MR Gazzara, Y Barash - Bioinformatics, 2018 - academic.oup.com
Analysis of RNA sequencing (RNA-Seq) data have highlighted the fact that most genes
undergo alternative splicing (AS) and that these patterns are tightly regulated. Many of these …
undergo alternative splicing (AS) and that these patterns are tightly regulated. Many of these …
spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data
Background RNA-seq data is currently underutilized, in part because it is difficult to predict
the functional impact of alternate transcription events. Recent software improvements in full …
the functional impact of alternate transcription events. Recent software improvements in full …
SNPlice: variants that modulate Intron retention from RNA-sequencing data
Rationale: The growing recognition of the importance of splicing, together with rapidly
accumulating RNA-sequencing data, demand robust high-throughput approaches, which …
accumulating RNA-sequencing data, demand robust high-throughput approaches, which …
Two-pass alignment improves novel splice junction quantification
BA Veeneman, S Shukla, SM Dhanasekaran… - …, 2016 - academic.oup.com
Motivation: Discovery of novel splicing from RNA sequence data remains a critical and
exciting focus of transcriptomics, but reduced alignment power impedes expression …
exciting focus of transcriptomics, but reduced alignment power impedes expression …
MapSplice: accurate mapping of RNA-seq reads for splice junction discovery
K Wang, D Singh, Z Zeng, SJ Coleman… - Nucleic acids …, 2010 - academic.oup.com
The accurate mapping of reads that span splice junctions is a critical component of all
analytic techniques that work with RNA-seq data. We introduce a second generation splice …
analytic techniques that work with RNA-seq data. We introduce a second generation splice …
Discerning novel splice junctions derived from RNA-seq alignment: a deep learning approach
Y Zhang, X Liu, J MacLeod, J Liu - BMC genomics, 2018 - Springer
Background Exon splicing is a regulated cellular process in the transcription of protein-
coding genes. Technological advancements and cost reductions in RNA sequencing have …
coding genes. Technological advancements and cost reductions in RNA sequencing have …