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Enrichment analysis with EpiAnnotator
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| Zeitschriftentitel: | Bioinformatics |
|---|---|
| Personen und Körperschaften: | , , |
| In: | Bioinformatics, 34, 2018, 10, S. 1781-1783 |
| Format: | E-Article |
| Sprache: | Englisch |
| veröffentlicht: |
Oxford University Press (OUP)
|
| Schlagwörter: |
| author_facet |
Pageaud, Yoann Plass, Christoph Assenov, Yassen Pageaud, Yoann Plass, Christoph Assenov, Yassen |
|---|---|
| author |
Pageaud, Yoann Plass, Christoph Assenov, Yassen |
| spellingShingle |
Pageaud, Yoann Plass, Christoph Assenov, Yassen Bioinformatics Enrichment analysis with EpiAnnotator Computational Mathematics Computational Theory and Mathematics Computer Science Applications Molecular Biology Biochemistry Statistics and Probability |
| author_sort |
pageaud, yoann |
| spelling |
Pageaud, Yoann Plass, Christoph Assenov, Yassen 1367-4803 1367-4811 Oxford University Press (OUP) Computational Mathematics Computational Theory and Mathematics Computer Science Applications Molecular Biology Biochemistry Statistics and Probability http://dx.doi.org/10.1093/bioinformatics/bty007 <jats:title>Abstract</jats:title> <jats:sec> <jats:title>Motivation</jats:title> <jats:p>Deciphering relevant biological insights from epigenomic data can be a challenging task. One commonly used approach is to perform enrichment analysis. However, finding, downloading and using the publicly available functional annotations require time, programming skills and IT infrastructure. Here we describe the online tool EpiAnnotator for performing enrichment analyses on epigenomic data in a fast and user-friendly way.</jats:p> </jats:sec> <jats:sec> <jats:title>Results</jats:title> <jats:p>EpiAnnotator is an R Package accompanied by a web interface. It contains regularly updated annotations from 4 public databases: Blueprint, RoadMap, GENCODE and the UCSC Genome Browser. Annotations are hosted locally or in a server environment and automatically updated by scripts of our own design. Thousands of tracks are available, reflecting data on a variety of tissues, cell types and cell lines from the human and mouse genomes. Users need to upload sets of selected and background regions. Results are displayed in customizable and easily interpretable figures.</jats:p> </jats:sec> <jats:sec> <jats:title>Availability and implementation</jats:title> <jats:p>The R package and Shiny app are open source and available under the GPL v3 license. EpiAnnotator’s web interface is accessible at http://computational-epigenomics.com/en/epiannotator.</jats:p> </jats:sec> Enrichment analysis with EpiAnnotator Bioinformatics |
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Oxford University Press (OUP), 2018 |
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Oxford University Press (OUP), 2018 |
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Bioinformatics |
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| title |
Enrichment analysis with EpiAnnotator |
| title_unstemmed |
Enrichment analysis with EpiAnnotator |
| title_full |
Enrichment analysis with EpiAnnotator |
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Enrichment analysis with EpiAnnotator |
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Enrichment analysis with EpiAnnotator |
| title_short |
Enrichment analysis with EpiAnnotator |
| title_sort |
enrichment analysis with epiannotator |
| topic |
Computational Mathematics Computational Theory and Mathematics Computer Science Applications Molecular Biology Biochemistry Statistics and Probability |
| url |
http://dx.doi.org/10.1093/bioinformatics/bty007 |
| publishDate |
2018 |
| physical |
1781-1783 |
| description |
<jats:title>Abstract</jats:title>
<jats:sec>
<jats:title>Motivation</jats:title>
<jats:p>Deciphering relevant biological insights from epigenomic data can be a challenging task. One commonly used approach is to perform enrichment analysis. However, finding, downloading and using the publicly available functional annotations require time, programming skills and IT infrastructure. Here we describe the online tool EpiAnnotator for performing enrichment analyses on epigenomic data in a fast and user-friendly way.</jats:p>
</jats:sec>
<jats:sec>
<jats:title>Results</jats:title>
<jats:p>EpiAnnotator is an R Package accompanied by a web interface. It contains regularly updated annotations from 4 public databases: Blueprint, RoadMap, GENCODE and the UCSC Genome Browser. Annotations are hosted locally or in a server environment and automatically updated by scripts of our own design. Thousands of tracks are available, reflecting data on a variety of tissues, cell types and cell lines from the human and mouse genomes. Users need to upload sets of selected and background regions. Results are displayed in customizable and easily interpretable figures.</jats:p>
</jats:sec>
<jats:sec>
<jats:title>Availability and implementation</jats:title>
<jats:p>The R package and Shiny app are open source and available under the GPL v3 license. EpiAnnotator’s web interface is accessible at http://computational-epigenomics.com/en/epiannotator.</jats:p>
</jats:sec> |
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| author | Pageaud, Yoann, Plass, Christoph, Assenov, Yassen |
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| description | <jats:title>Abstract</jats:title> <jats:sec> <jats:title>Motivation</jats:title> <jats:p>Deciphering relevant biological insights from epigenomic data can be a challenging task. One commonly used approach is to perform enrichment analysis. However, finding, downloading and using the publicly available functional annotations require time, programming skills and IT infrastructure. Here we describe the online tool EpiAnnotator for performing enrichment analyses on epigenomic data in a fast and user-friendly way.</jats:p> </jats:sec> <jats:sec> <jats:title>Results</jats:title> <jats:p>EpiAnnotator is an R Package accompanied by a web interface. It contains regularly updated annotations from 4 public databases: Blueprint, RoadMap, GENCODE and the UCSC Genome Browser. Annotations are hosted locally or in a server environment and automatically updated by scripts of our own design. Thousands of tracks are available, reflecting data on a variety of tissues, cell types and cell lines from the human and mouse genomes. Users need to upload sets of selected and background regions. Results are displayed in customizable and easily interpretable figures.</jats:p> </jats:sec> <jats:sec> <jats:title>Availability and implementation</jats:title> <jats:p>The R package and Shiny app are open source and available under the GPL v3 license. EpiAnnotator’s web interface is accessible at http://computational-epigenomics.com/en/epiannotator.</jats:p> </jats:sec> |
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| imprint | Oxford University Press (OUP), 2018 |
| imprint_str_mv | Oxford University Press (OUP), 2018 |
| institution | DE-D275, DE-Bn3, DE-Brt1, DE-Zwi2, DE-D161, DE-Gla1, DE-Zi4, DE-15, DE-Rs1, DE-Pl11, DE-105, DE-14, DE-Ch1, DE-L229 |
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| spelling | Pageaud, Yoann Plass, Christoph Assenov, Yassen 1367-4803 1367-4811 Oxford University Press (OUP) Computational Mathematics Computational Theory and Mathematics Computer Science Applications Molecular Biology Biochemistry Statistics and Probability http://dx.doi.org/10.1093/bioinformatics/bty007 <jats:title>Abstract</jats:title> <jats:sec> <jats:title>Motivation</jats:title> <jats:p>Deciphering relevant biological insights from epigenomic data can be a challenging task. One commonly used approach is to perform enrichment analysis. However, finding, downloading and using the publicly available functional annotations require time, programming skills and IT infrastructure. Here we describe the online tool EpiAnnotator for performing enrichment analyses on epigenomic data in a fast and user-friendly way.</jats:p> </jats:sec> <jats:sec> <jats:title>Results</jats:title> <jats:p>EpiAnnotator is an R Package accompanied by a web interface. It contains regularly updated annotations from 4 public databases: Blueprint, RoadMap, GENCODE and the UCSC Genome Browser. Annotations are hosted locally or in a server environment and automatically updated by scripts of our own design. Thousands of tracks are available, reflecting data on a variety of tissues, cell types and cell lines from the human and mouse genomes. Users need to upload sets of selected and background regions. Results are displayed in customizable and easily interpretable figures.</jats:p> </jats:sec> <jats:sec> <jats:title>Availability and implementation</jats:title> <jats:p>The R package and Shiny app are open source and available under the GPL v3 license. EpiAnnotator’s web interface is accessible at http://computational-epigenomics.com/en/epiannotator.</jats:p> </jats:sec> Enrichment analysis with EpiAnnotator Bioinformatics |
| spellingShingle | Pageaud, Yoann, Plass, Christoph, Assenov, Yassen, Bioinformatics, Enrichment analysis with EpiAnnotator, Computational Mathematics, Computational Theory and Mathematics, Computer Science Applications, Molecular Biology, Biochemistry, Statistics and Probability |
| title | Enrichment analysis with EpiAnnotator |
| title_full | Enrichment analysis with EpiAnnotator |
| title_fullStr | Enrichment analysis with EpiAnnotator |
| title_full_unstemmed | Enrichment analysis with EpiAnnotator |
| title_short | Enrichment analysis with EpiAnnotator |
| title_sort | enrichment analysis with epiannotator |
| title_unstemmed | Enrichment analysis with EpiAnnotator |
| topic | Computational Mathematics, Computational Theory and Mathematics, Computer Science Applications, Molecular Biology, Biochemistry, Statistics and Probability |
| url | http://dx.doi.org/10.1093/bioinformatics/bty007 |