Internet Archive Scholar

HPAanalyze: an R package that facilitates the retrieval and analysis of the Human Protein Atlas data

Anh Nhat Tran, Alex M. Dussaq, Timothy Kennell, Christopher D. Willey, Anita B. Hjelmeland
<span title="2019-09-09">2019</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;

Preserved Fulltext

fulltext thumbnail
Web Archive Capture PDF (2.6 MB)
https://web.archive.org/web/20200216135049/https://link.springer.com/content/pdf/10.1186%2Fs12859-019-3059-z.pdf

A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit <a rel="external noopener" href="https://link.springer.com/content/pdf/10.1186%2Fs12859-019-3059-z.pdf">the original URL</a>. The file type is <code>application/pdf</code>.

The Human Protein Atlas (HPA) aims to map human proteins via multiple technologies including imaging, proteomics and transcriptomics. Access of the HPA data is mainly via web-based interface allowing views of individual proteins, which may not be optimal for data analysis of a gene set, or automatic retrieval of original images. Results: HPAanalyze is an R package for retrieving and performing exploratory analysis of data from HPA. HPAanalyze provides functionality for importing data tables and
more &raquo; ... xml files from HPA, exporting and visualizing data, as well as downloading all staining images of interest. The package is free, open source, and available via Bioconductor and GitHub. We provide examples of the use of HPAanalyze to investigate proteins altered in the deadly brain tumor glioblastoma. For example, we confirm Epidermal Growth Factor Receptor elevation and Phosphatase and Tensin Homolog loss and suggest the importance of the GTP Cyclohydrolase I/ Tetrahydrobiopterin pathway. Additionally, we provide an interactive website for non-programmers to explore and visualize data without the use of R. Conclusions: HPAanalyze integrates into the R workflow with the tidyverse framework, and it can be used in combination with Bioconductor packages for easy analysis of HPA data.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-019-3059-z">doi:10.1186/s12859-019-3059-z</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/agbmreqx5baozgxnshsjl3zrrm">fatcat:agbmreqx5baozgxnshsjl3zrrm</a> </span>
<span class="ui label basic orange small" title="Directory of Open Access Journals">DOAJ</span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200216135049/https://link.springer.com/content/pdf/10.1186%2Fs12859-019-3059-z.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/34/36/3436c684c2fd510078b8728ade7be5156d43edac.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-019-3059-z"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a>
Citation

Anh Nhat Tran, Alex M. Dussaq, Timothy Kennell, Christopher D. Willey, Anita B. Hjelmeland. "HPAanalyze: an R package that facilitates the retrieval and analysis of the Human Protein Atlas data." BMC Bioinformatics 20.1 (2019)