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Researchers from the Beijing Forestry University have developed a clustering mixture model to discover distinct groups of genes expressed du...

Researchers from the Beijing Forestry University have developed a clustering mixture model to discover distinct groups of genes expressed du...

A flexible Bayesian method for detecting allelic imbalance in RNA-seq data | RNA-Seq Blog

A flexible Bayesian method for detecting allelic imbalance in RNA-seq data | RNA-Seq Blog

XSAnno – a framework for building ortholog models in cross-species transcriptome comparisons | RNA-Seq Blog

XSAnno – a framework for building ortholog models in cross-species transcriptome comparisons | RNA-Seq Blog

MicroRNAs represent an important class of small non-coding RNAs regulating gene expression in eukaryotes. Present algorithms typically rely ...

MicroRNAs represent an important class of small non-coding RNAs regulating gene expression in eukaryotes. Present algorithms typically rely ...

Scrimer – designing primers from transcriptome data - Here researchers from the Charles University in Prague present a pipeline called Scrimer that automates multiple steps, including adaptor removal, read mapping, selection of SNPs, and multiple primer design from transcriptome data. The designed primers can be used in conjunction with several widely-used genotyping methods such as SNaPshot or MALDI-TOF genotyping. Scrimer is composed of several reusable modules and an interactive bash…

Scrimer – designing primers from transcriptome data - Here researchers from the Charles University in Prague present a pipeline called Scrimer that automates multiple steps, including adaptor removal, read mapping, selection of SNPs, and multiple primer design from transcriptome data. The designed primers can be used in conjunction with several widely-used genotyping methods such as SNaPshot or MALDI-TOF genotyping. Scrimer is composed of several reusable modules and an interactive bash…

TEtranscripts – A package for including transposable elements in differential expression analysis of RNA-Seq datasets - Researchers from Cold Spring Harbor Laboratory have developed a method and software package for including both gene- and TE-associated ambiguously mapped reads in differential expression analysis. This method shows improved recovery of TE transcripts over other published expression analysis methods, in both synthetic data and qPCR/NanoString-validated published datasets...

TEtranscripts – A package for including transposable elements in differential expression analysis of RNA-Seq datasets - Researchers from Cold Spring Harbor Laboratory have developed a method and software package for including both gene- and TE-associated ambiguously mapped reads in differential expression analysis. This method shows improved recovery of TE transcripts over other published expression analysis methods, in both synthetic data and qPCR/NanoString-validated published datasets...

DeTCT – a purely quantitative digital gene expression sample processing and analysis package - Researchers at the Wellcome Trust Sanger Institute present a purely quantitative digital gene expression sample processing and analysis package called differential expression transcript counting technique (DeTCT) that begins with tissue samples and produces a text table or HTML table, comprising genomic coordinates representing the 3′ ends of genes, raw and normalised counts, and a fold change...

DeTCT – a purely quantitative digital gene expression sample processing and analysis package - Researchers at the Wellcome Trust Sanger Institute present a purely quantitative digital gene expression sample processing and analysis package called differential expression transcript counting technique (DeTCT) that begins with tissue samples and produces a text table or HTML table, comprising genomic coordinates representing the 3′ ends of genes, raw and normalised counts, and a fold change...

Researchers at the University of North Carolina at Chapel Hill propose a novel RNA-Seq quantification method, RNA-Skim, which partitions the...

Researchers at the University of North Carolina at Chapel Hill propose a novel RNA-Seq quantification method, RNA-Skim, which partitions the...

Tailor – a computational framework for detecting non-templated tailing of small silencing RNAs - Small silencing RNAs, including microRNAs, endogenous small interfering RNAs (endo-siRNAs) and Piwi-interacting RNAs (piRNAs), have been shown to play important roles in fine-tuning gene expression, defending virus and controlling transposons. Loss of small silencing RNAs or components in their pathways often leads to severe developmental defects, including lethality and sterility. Recently…

Tailor – a computational framework for detecting non-templated tailing of small silencing RNAs - Small silencing RNAs, including microRNAs, endogenous small interfering RNAs (endo-siRNAs) and Piwi-interacting RNAs (piRNAs), have been shown to play important roles in fine-tuning gene expression, defending virus and controlling transposons. Loss of small silencing RNAs or components in their pathways often leads to severe developmental defects, including lethality and sterility. Recently…

zflncRNApedia – A Comprehensive Online Resource for Zebrafish Long Non-Coding RNAs - Recent transcriptome annotation using deep sequencing approaches have annotated a large number of long non-coding RNAs in zebrafish, a popular model organism for human diseases. These studies characterized lncRNAs in critical developmental stages as well as adult tissues. Each of the studies has uncovered a distinct set of lncRNAs, with minor over...

zflncRNApedia – A Comprehensive Online Resource for Zebrafish Long Non-Coding RNAs - Recent transcriptome annotation using deep sequencing approaches have annotated a large number of long non-coding RNAs in zebrafish, a popular model organism for human diseases. These studies characterized lncRNAs in critical developmental stages as well as adult tissues. Each of the studies has uncovered a distinct set of lncRNAs, with minor over...

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