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BioWardrobe: an integrated platform for analysis of epigenomics and transcriptomics data
High-throughput sequencing has revolutionized biology by enhancing our ability to perform genome-wide studies. However, due to lack of bioinformatics expertise, modern technologies are still beyond the capabilities of many laboratories. Herein, we present the BioWardrobe platform, which allows users...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4531538/ https://www.ncbi.nlm.nih.gov/pubmed/26248465 http://dx.doi.org/10.1186/s13059-015-0720-3 |
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author | Kartashov, Andrey V. Barski, Artem |
author_facet | Kartashov, Andrey V. Barski, Artem |
author_sort | Kartashov, Andrey V. |
collection | PubMed |
description | High-throughput sequencing has revolutionized biology by enhancing our ability to perform genome-wide studies. However, due to lack of bioinformatics expertise, modern technologies are still beyond the capabilities of many laboratories. Herein, we present the BioWardrobe platform, which allows users to store, visualize and analyze epigenomics and transcriptomics data using a biologist-friendly web interface, without the need for programming expertise. Predefined pipelines allow users to download data, visualize results on a genome browser, calculate RPKMs (reads per kilobase per million) and identify peaks. Advanced capabilities include differential gene expression and binding analysis, and creation of average tag -density profiles and heatmaps. BioWardrobe can be found at http://biowardrobe.com. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-015-0720-3) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-4531538 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-45315382015-08-12 BioWardrobe: an integrated platform for analysis of epigenomics and transcriptomics data Kartashov, Andrey V. Barski, Artem Genome Biol Software High-throughput sequencing has revolutionized biology by enhancing our ability to perform genome-wide studies. However, due to lack of bioinformatics expertise, modern technologies are still beyond the capabilities of many laboratories. Herein, we present the BioWardrobe platform, which allows users to store, visualize and analyze epigenomics and transcriptomics data using a biologist-friendly web interface, without the need for programming expertise. Predefined pipelines allow users to download data, visualize results on a genome browser, calculate RPKMs (reads per kilobase per million) and identify peaks. Advanced capabilities include differential gene expression and binding analysis, and creation of average tag -density profiles and heatmaps. BioWardrobe can be found at http://biowardrobe.com. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-015-0720-3) contains supplementary material, which is available to authorized users. BioMed Central 2015-08-07 2015 /pmc/articles/PMC4531538/ /pubmed/26248465 http://dx.doi.org/10.1186/s13059-015-0720-3 Text en © Kartashov and Barski. 2015 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Software Kartashov, Andrey V. Barski, Artem BioWardrobe: an integrated platform for analysis of epigenomics and transcriptomics data |
title | BioWardrobe: an integrated platform for analysis of epigenomics and transcriptomics data |
title_full | BioWardrobe: an integrated platform for analysis of epigenomics and transcriptomics data |
title_fullStr | BioWardrobe: an integrated platform for analysis of epigenomics and transcriptomics data |
title_full_unstemmed | BioWardrobe: an integrated platform for analysis of epigenomics and transcriptomics data |
title_short | BioWardrobe: an integrated platform for analysis of epigenomics and transcriptomics data |
title_sort | biowardrobe: an integrated platform for analysis of epigenomics and transcriptomics data |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4531538/ https://www.ncbi.nlm.nih.gov/pubmed/26248465 http://dx.doi.org/10.1186/s13059-015-0720-3 |
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