Statistical Modeling of RNA-Seq Data.

ToNER: A tool for identifying nucleotide enrichment signals in feature-enriched RNA-seq data

BACKGROUND Biochemical methods are available for enriching 5' ends of RNAs in prokaryotes, which are employed in the differential RNA-seq (dRNA-seq) and the more recent Cappable-seq protocols. Computational methods are needed to locate RNA 5' ends from these data by statistical analysis of the enrichment. Although statistical-based analysis methods have been developed for dRNA-seq, they may not...

Msiq: Joint Modeling of Multiple Rna-seq Samples for Accurate Isoform Quantification by Wei

Next-generation RNA sequencing (RNA-seq) technology has been widely used to assess full-length RNA isoform abundance in a highthroughput manner. RNA-seq data offer insight into gene expression levels and transcriptome structures, enabling us to better understand the regulation of gene expression and fundamental biological processes. Accurate isoform quantification from RNA-seq data is challengi...

Sparse linear modeling of next-generation mRNA sequencing (RNA-Seq) data for isoform discovery and abundance estimation.

Since the inception of next-generation mRNA sequencing (RNA-Seq) technology, various attempts have been made to utilize RNA-Seq data in assembling full-length mRNA isoforms de novo and estimating abundance of isoforms. However, for genes with more than a few exons, the problem tends to be challenging and often involves identifiability issues in statistical modeling. We have developed a statisti...

STATISTICAL MODELING OF RNA-SEQ DATA By

Flexible analysis of transcriptome assemblies with Ballgown

A key advantage of RNA sequencing (RNA-seq) over hybridization-based technologies such as microarrays is that RNA-seq makes it possible to reconstruct complete gene structures, including multiple splice variants, from raw RNA-seq reads without relying on previouslyestablished annotations [20, 32, 9]. But with this added flexibility, there are increased computational demands on upstream processi...