RNA-Seq Blog Transcriptome Research & Industry News
Long non-coding RNAs (lncRNAs) are an emerging class of non-coding RNAs and potent regulatory elements in the living cells. High throughput RNA...
Read More »lncRNADetector – a bioinformatics pipeline for long noncoding RNA identification
lncEvo – automated identification and conservation study of long noncoding RNAs
Long noncoding RNAs represent a large class of transcripts with two common features: they exceed an arbitrary length threshold of 200 nt and are...
Read More »Cerina – systematic circRNA functional annotation based on integrative analysis of ceRNA interactions
Circular RNAs, a family of covalently circularized RNAs with tissue-specific expression, were recently demonstrated to play important roles in mammalian biology. Regardless of extensive research to predict...
Read More »MetaTX -new model solves problem of isoform ambiguity
A new statistical model from Xi’an Jiaotong-Liverpool University aims to solve the problem of isoform ambiguity related to RNA modifications. The paper, published on 2 November in the leading...
Read More »TransSynW – A single‐cell RNA‐sequencing based web application to guide cell conversion experiments
Generation of desired cell types by cell conversion remains a challenge. In particular, derivation of novel cell subtypes identified by single‐cell technologies will open up new strategies for cell therapies. The recent increase in the generation of single‐cell RNA‐sequencing (scRNA‐seq) ...
Read More »Immunedeconv – an R package for unified access to computational methods for estimating immune cell fractions from bulk RNA-seq data
The composition and density of immune cells in the tumor microenvironment (TME) profoundly influence tumor progression and success of anti-cancer therapies. Flow cytometry, immunohistochemistry staining or single-cell sequencing are often unavailable such that we rely on computational methods to estimate ...
Read More »ORFquant – annotation and quantification of translation at the level of single open reading frames
Translation has a fundamental function in defining the fate of the transcribed genome. RNA-sequencing (RNA-seq) data enable the quantification of complex transcript mixtures, often detecting several transcript isoforms of unknown functions for one gene...
Read More »Researchers improve the annotation of disease-relevant genes in RNA-sequencing data
Growing evidence suggests that human gene annotation remains incomplete; however, it is unclear how this affects different tissues and our understanding of different disorders. A team led by researchers at University College London detect...
Read More »CICERO – a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data
To discover driver fusions beyond canonical exon-to-exon chimeric transcripts, researchers at St. Jude Children’s Research Hospital have developed CICERO, a local assembly-based algorithm that integrates...
Read More »Identifying cell types from single-cell RNA sequencing data
Identifying different types of cells within a tissue or an organ can be very challenging and time-consuming. Methods to identify cell types from single-cell RNA sequencing data have been...
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