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Heat*seq: an interactive web tool for high-throughput sequencing experiment comparison with public data

Summary: Better protocols and decreasing costs have made high-throughput sequencing experiments 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 freely available in the public domain m...

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Detalles Bibliográficos
Autores principales: Devailly, Guillaume, Mantsoki, Anna, Joshi, Anagha
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5079476/
https://www.ncbi.nlm.nih.gov/pubmed/27378302
http://dx.doi.org/10.1093/bioinformatics/btw407
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author Devailly, Guillaume
Mantsoki, Anna
Joshi, Anagha
author_facet Devailly, Guillaume
Mantsoki, Anna
Joshi, Anagha
author_sort Devailly, Guillaume
collection PubMed
description Summary: Better protocols and decreasing costs have made high-throughput sequencing experiments 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 freely available in the public domain might be limited due to lack of bioinformatics expertise. Though several tools, including genome browsers, allow such comparison at a single gene level, they do not provide a genome-wide view. We developed Heat*seq, a web-tool that allows genome scale comparison of high throughput experiments chromatin immuno-precipitation followed by sequencing, RNA-sequencing and Cap Analysis of Gene Expression) provided by a user, to the data in the public domain. Heat*seq currently contains over 12 000 experiments across diverse tissues and cell types in human, mouse and drosophila. Heat*seq displays interactive correlation heatmaps, with an ability to dynamically subset datasets to contextualize user experiments. High quality figures and tables are produced and can be downloaded in multiple formats. Availability and Implementation: Web application: http://www.heatstarseq.roslin.ed.ac.uk/. Source code: https://github.com/gdevailly. Contact: Guillaume.Devailly@roslin.ed.ac.uk or Anagha.Joshi@roslin.ed.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
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spelling pubmed-50794762016-10-26 Heat*seq: an interactive web tool for high-throughput sequencing experiment comparison with public data Devailly, Guillaume Mantsoki, Anna Joshi, Anagha Bioinformatics Applications Notes Summary: Better protocols and decreasing costs have made high-throughput sequencing experiments 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 freely available in the public domain might be limited due to lack of bioinformatics expertise. Though several tools, including genome browsers, allow such comparison at a single gene level, they do not provide a genome-wide view. We developed Heat*seq, a web-tool that allows genome scale comparison of high throughput experiments chromatin immuno-precipitation followed by sequencing, RNA-sequencing and Cap Analysis of Gene Expression) provided by a user, to the data in the public domain. Heat*seq currently contains over 12 000 experiments across diverse tissues and cell types in human, mouse and drosophila. Heat*seq displays interactive correlation heatmaps, with an ability to dynamically subset datasets to contextualize user experiments. High quality figures and tables are produced and can be downloaded in multiple formats. Availability and Implementation: Web application: http://www.heatstarseq.roslin.ed.ac.uk/. Source code: https://github.com/gdevailly. Contact: Guillaume.Devailly@roslin.ed.ac.uk or Anagha.Joshi@roslin.ed.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. Oxford University Press 2016-11-01 2016-07-04 /pmc/articles/PMC5079476/ /pubmed/27378302 http://dx.doi.org/10.1093/bioinformatics/btw407 Text en © The Author 2016. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Applications Notes
Devailly, Guillaume
Mantsoki, Anna
Joshi, Anagha
Heat*seq: an interactive web tool for high-throughput sequencing experiment comparison with public data
title Heat*seq: an interactive web tool for high-throughput sequencing experiment comparison with public data
title_full Heat*seq: an interactive web tool for high-throughput sequencing experiment comparison with public data
title_fullStr Heat*seq: an interactive web tool for high-throughput sequencing experiment comparison with public data
title_full_unstemmed Heat*seq: an interactive web tool for high-throughput sequencing experiment comparison with public data
title_short Heat*seq: an interactive web tool for high-throughput sequencing experiment comparison with public data
title_sort heat*seq: an interactive web tool for high-throughput sequencing experiment comparison with public data
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5079476/
https://www.ncbi.nlm.nih.gov/pubmed/27378302
http://dx.doi.org/10.1093/bioinformatics/btw407
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