Expression and Quantification

RNA sequencing (RNA-seq) is emerging as a critical approach in biological research. However, its high-throughput advantage is significantly limited by the capacity of bioinformatics tools. The research community urgently needs user-friendly tools to efficiently analyze the complicated data generated by ...

Alternative splicing is the main mechanism governing protein diversity. The recent developments in RNA-Seq technology have enabled the study of the global impact and regulation of this biological process. However, the lack of standardized protocols constitutes a major bottleneck in ...

An overview of the SAMCNet package (available at https://github.com/binarybana/samcnet) that implements optimal Bayesian classification for RNA-Seq data as part of an upcoming publication. (Publication details will follow once reviewed and accepted)

SeqGSEA is an open-source Bioconductor package, for the functional integration of differential expression and splicing analysis in RNA-Seq data. SeqGSEA implements an analysis pipeline which first computes differential splicing (DS) and differential expression (DE) scores, followed by integrating them into ...

Measuring expression levels of genes at the whole genome level can be useful for many purposes, especially for revealing biological pathways underlying specific phenotype conditions. When gene expression is measured over a time period, we have opportunities to understand how ...

One of the concerns of assembling de novo transcriptomes is determining the amount of read sequences required to ensure a comprehensive coverage of genes expressed in a particular sample. In this report, researchers from the Rubber Research Institute of Malaysia ...

Several outlier and subgroup identification statistics (OASIS) have been proposed to discover transcriptomic features with outliers or multiple modes in expression that are indicative of distinct biological processes or subgroups. Here, researchers from the St. Jude Children’s Research Hospital, Memphis borrow ...

Gene expression measurements have successfully been used for building prognostic signatures, i.e for identifying a short list of important genes that can predict patient outcome. Mostly microarray measurements have been considered, and there is little advice available for building multivariable ...

A team led by researchers at the Memorial Sloan-Kettering Cancer Center present Oqtans, an open-source workbench for quantitative transcriptome analysis, that is integrated in the Galaxy framework. Its distinguishing features include customizable computational workflows and a modular pipeline architecture that ...

In the last decade, Next-Generation Sequencing technologies have been extensively applied to quantitative transcriptomics, making RNA sequencing a valuable alternative to microarrays for measuring and comparing gene transcription levels. Although several methods have been proposed to provide an unbiased estimate ...