Data Analysis

miRSeq – A User-Friendly Standalone Toolkit for Sequencing Quality Evaluation and miRNA Profiling

rna-seq

MicroRNAs (miRNAs) present diverse regulatory functions in a wide range of biological activities. Studies on miRNA functions generally depend on determining miRNA expression profiles between libraries by using a next-generation sequencing (NGS) platform. Currently, several online web services are developed ...

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Visualization of nucleotide substitutions in the (micro)transcriptome

rna-seq

RNA-related applications of the next-generation sequencing (NGS) technologies require context-specific interpretations: e.g., sequence mismatches may indicate sites of RNA editing, or uneven read coverage often points to mature form of microRNA. Existing visualization tools traditionally show RNA molecules in two ...

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SLaP Mapper: a webserver for identifying and quantifying spliced-leader addition and polyadenylation site usage

rna-seq

The Kinetoplastida are a diverse and globally distributed class of free-living and parasitic single-celled eukaryotes that collectively cause a significant burden on human health and welfare. In kinetoplastids individual genes do not have promoters, but rather all genes are arranged ...

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shRNA-seq data analysis with edgeR

rna-seq

Pooled short hairpin RNA sequencing (shRNA-seq) screens are becoming increasingly popular in functional genomics research, and there is a need to establish optimal analysis tools to handle such data. This open-source shRNA processing pipeline in edgeR provides a complete analysis ...

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SCOPE++ : Sequence Classification Of homoPolymer Emissions

rna-seq

mRNA polyadenylation, the addition of a poly(A) tail to the 3′-end of pre-mRNA, is a process critical to gene expression and regulation in eukaryotes. To understand the molecular mechanisms governing polyadenylation and other relevant biological processes, it is important to ...

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Long Intergenic Non-Coding RNAs (LincRNAs) Identified by RNA-Seq

rna-seq

In an attempt to find breast cancer tissue and respective adjacent normal tissue were studied for the expression of lincRNAs by RNA-seq. Among the 538 lincRNAs studied, 124 lincRNAs were exclusively expressed in cancer adjacent tissues and 62 lincRNAs were ...

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Circleator: Flexible Circular Visualization of Genome-Associated Data

rna-seq

Circleator is a Perl application that generates circular figures of genome-associated data. It leverages BioPerl to support standard annotation and sequence file formats and produces publication-quality SVG output. It is designed to be both flexible and easy to use. It ...

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Corset – differential gene expression analysis for de novo assembled transcriptomes

rna-seq

Next generation sequencing has made it possible to perform differential gene expression studies in non-model organisms. For these studies, the need for a reference genome is circumvented by performing de novo assembly on the RNA-seq data. However, transcriptome assembly produces ...

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Calling genotypes from public RNA-sequencing data enables identification of genetic variants that affect gene-expression levels

rna-seq

Given increasing numbers of RNA-seq samples in the public domain, researchers at the University of Groningen studied to what extent expression quantitative trait loci (eQTLs) and allele-specific expression (ASE) can be identified in public RNA-seq data while also deriving the ...

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Researchers Develop Tool to Better Visualize, Analyze Human Genomic & Transcriptomic Data

rna-seq

Scientists at the University of Maryland have developed a new, web-based tool that enables researchers to quickly and easily visualize and compare large amounts of genomic information resulting from high-throughput sequencing experiments. The free tool, called Epiviz, was described in ...

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