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Strategies for transcriptional splice variant detection

Strategies for transcriptional splice variant detection

The advent and improvement of high-throughput sequencing over the past decade leveraged the study of whole genomes and transcriptomes of different organisms at lower costs. In transcriptomics, RNA-Seq expands our capacity to understand gene expression in different tissues and pathologies, ...

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QuasR – Quantification and annotation of short reads in R

QuasR – Quantification and annotation of short reads in R

QuasR is a package for the integrated analysis of high-throughput sequencing data in R, covering all steps from read preprocessing, alignment and quality control to quantification. QuasR supports different experiment types (including RNA-seq, ChIP-seq and Bis-seq) and analysis variants (e.g. ...

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A ratiometric-based measure of gene co-expression

A ratiometric-based measure of gene co-expression

Gene co-expression analysis has previously been based on measures that include correlation coefficients and mutual information, as well as newcomers such as MIC. These measures depend primarily on the degree of association between the RNA levels of two genes and ...

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CLASS – Splice Variant Annotation from RNA-Seq Reads

CLASS – 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 capture splicing variation accurately has proven difficult. Current programs find major isoforms of a gene but ...

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