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With the establishment of better protocols and decreasing costs, high-throughput sequencing experiments such as RNA-seq or ChIP-seq are now accessible even to small experimental laboratories. However, comparing one or few experiments generated by an individual lab to the vast amount of relevant data available in public domain might be hindered due to lack of bioinformatics expertise. Though several user friendly tools allow such comparison gene or promoter level, a genome-wide picture is missing. We developed Heat*seq, a free, open-source web-tool that allows comparison at genome-wide scale of any experiments provided by the user to public datasets (RNA-seq, ChIP-seq and CAGE experiments from Bgee, Blueprint epigenome, CODEX, ENCODE, FANTOM5, FlyBase, modEncode, and Roadmap epigenomics) in human, mouse and drosophila. Correlation coefficients amongst experiments is displayed as an interactive correlation heatmaps. Users can thus identify clusters of experiments in public domain similar to their experiment in minutes through a user-friendly interface. This fast interactive web-application uses the R/shiny framework allowing the generation of high-quality figures and tables that can be easily downloaded in multiple formats. Heat*seq is freely available at http://www.heatstarseq.roslin.ed.ac.uk/.
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With the establishment of better protocols and decreasing costs, high-throughput sequencing experiments such as RNA-seq or ChIP-seq are now accessible even to small experimental laboratories. However, comparing one or few experiments generated by an individual lab to the vast amount of relevant data available in public domain might be hindered due to lack of bioinformatics expertise. Though several user friendly tools allow such comparison gene or promoter level, a genome-wide picture is missing. We developed Heat*seq, a free, open-source web-tool that allows comparison at genome-wide scale of any experiments provided by the user to public datasets (RNA-seq, ChIP-seq and CAGE experiments from Bgee, Blueprint epigenome, CODEX, ENCODE, FANTOM5, FlyBase, modEncode, and Roadmap epigenomics) in human, mouse and drosophila. Correlation coefficients amongst experiments is displayed as an interactive correlation heatmaps. Users can thus identify clusters of experiments in public domain similar to their experiment in minutes through a user-friendly interface. This fast interactive web-application uses the R/shiny framework allowing the generation of high-quality figures and tables that can be easily downloaded in multiple formats. Heat*seq is freely available at http://www.heatstarseq.roslin.ed.ac.uk/.
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  • Other
We are developing a customized version of Galaxy called G-OnRamp that will enable biologists to annotate the functional elements of eukaryotic genomes using large genomic datasets, a task that can also serve as an introduction to other “big data” biomedical analyses. Genome annotation—identifying functionally active regions within a genome—requires the use of diverse datasets and tools, including sequence similarity to known genes, gene prediction models, and high-throughput genomic data. To construct this interactive Web-based environment for genome annotation, we are building on two successful efforts, the Genomics Education Partnership (GEP) and Galaxy. GEP (http://gep.wustl.edu) is a consortium of over 100 colleges/universities that provides classroom undergraduate research experiences in genomics for students at all levels. Students perform primary research on selected regions of Drosophila genomes using genomic databases (e.g., FlyBase) and bioinformatics tools (e.g., BLAST) while learning about gene structure, evolution, programming, and other topics. GEP faculty are now interested in annotating other eukaryotic genomes, reflecting their diverse research interests. G-OnRamp will extend Galaxy by providing (a) analysis pipelines for functional genomic data (e.g., ChIP-Seq, RNA-Seq); (b) interactive visual analytics to annotate a genome (e.g., create UCSC Assembly Hubs); and (c) capacity for collaborative genome annotation. The GEP will serve as a key use case to validate and refine G-OnRamp, ensuring that it satisfies real educational needs. In this poster and demonstration, we will describe G-OnRamp’s vision and showcase its current features. G-OnRamp is available under the Academic Free License, and the software will be available via https://github.com/goeckslab
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