216 lines
7.9 KiB
Text
216 lines
7.9 KiB
Text
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<title>Home | ORIO</title>
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src="/static/js/ufa.min.js?agency=HHS&subagency=NIH"></script>
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<h2>ORIO: Online Resource for Integrative Omics</h2>
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<p>
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ORIO (Online Resource for Integrative Omics) is a platform for integration of
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whole genome data accessible to life scientists with minimal computational
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expertise. ORIO is implemented in a modern web framework that intuitively
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organizes data and analysis results. All features are accessible using its web
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interface; environmental health scientists and other users may upload data,
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set-up analyses, and view results all through an interactive GUI. ORIO hosts
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4,506 human and mouse datasets from the ENCODE research project, providing a
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point of access for life scientists to contextualize their own data within a
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rigorously controlled consortial dataset. Statistical tests are also implemented
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next to dynamic displays of analysis results, allowing transitions from
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discovery-based to hypothesis-based inquiries. ORIO was consciously designed to
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make minimal assumptions about data during analysis, allowing its applications
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to a variety of experiment types and study designs.
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</p>
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<h3>Citation</h3>
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<p>
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ORIO has been published in <a href=https://doi.org/10.1093/nar/gkx270>Lavender et al. 2017</a>
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<span class="glyphicon glyphicon-new-window"></span>.
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</p>
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<p>
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To cite in your publications:
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</p>
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<p>
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Lavender CA, Shapiro AJ, Burkholder AB, Bennett BD, Adelman K, Fargo DC. ORIO
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(Online Resource for Integrative Omics): a web-based platform for rapid
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integration of next generation sequencing data. Nucleic Acids Res. 2017 Jun 2;
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45 (10): 5678-5690. doi: 10.1093/nar/gkx270.
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</p>
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<h3>Example functionality</h3>
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<p>
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To show what ORIO has to offer, we've created five different examples. Details
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on each are described in the <a href=https://doi.org/10.1093/nar/gkx270>companion manuscript</a>
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<span class="glyphicon glyphicon-new-window"></span>.
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</p>
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<p>
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<a href=https://orio.niehs.nih.gov/dashboard/analysis/889-sample-validation-of-chip-seq-data/>Vignette 1</a>:
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Validation of experimental ChIP-seq data<br>
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<a href=https://orio.niehs.nih.gov/dashboard/analysis/850-sample-integration-over-chip-seq-peaks/>Vignette 2</a>:
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Characterization of ChIP-seq peaks by other NGS data<br>
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<a href=https://orio.niehs.nih.gov/dashboard/analysis/853-sample-correlation-with-gene-expression/>Vignette 3</a>:
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Correlation of gene expression with histone modification data<br>
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<a href=https://orio.niehs.nih.gov/dashboard/analysis/842-sample-recapitulation-of-cell-lineages/>Vignette 4</a>:
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Recapitulation of cell lineages using NGS data<br>
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<a href=https://orio.niehs.nih.gov/dashboard/analysis/855-sample-characterization-of-enhancers-and-promoters/>Vignette 5</a>:
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Investigation of genome-wide transcription<br>
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</p>
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