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drawProteins: a Bioconductor/R package for reproducible and programmatic generation of protein schematics
Protein schematics are valuable for research, teaching and knowledge communication. However, the tools used to automate the process are challenging. The purpose of the drawProteins package is to enable the generation of schematics of proteins in an automated fashion that can integrate with the Bioco...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
F1000 Research Limited
2018
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6107989/ https://www.ncbi.nlm.nih.gov/pubmed/30210791 http://dx.doi.org/10.12688/f1000research.14541.1 |
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author | Brennan, Paul |
author_facet | Brennan, Paul |
author_sort | Brennan, Paul |
collection | PubMed |
description | Protein schematics are valuable for research, teaching and knowledge communication. However, the tools used to automate the process are challenging. The purpose of the drawProteins package is to enable the generation of schematics of proteins in an automated fashion that can integrate with the Bioconductor/R suite of tools for bioinformatics and statistical analysis. Using UniProt accession numbers, the package uses the UniProt API to get the features of the protein from the UniProt database. The features are assembled into a data frame and visualized using adaptations of the ggplot2 package. Visualizations can be customised in many ways including adding additional protein features information from other data frames, altering colors and protein names and adding extra layers using other ggplot2 functions. This can be completed within a script that makes the workflow reproducible and sharable. |
format | Online Article Text |
id | pubmed-6107989 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | F1000 Research Limited |
record_format | MEDLINE/PubMed |
spelling | pubmed-61079892018-09-11 drawProteins: a Bioconductor/R package for reproducible and programmatic generation of protein schematics Brennan, Paul F1000Res Software Tool Article Protein schematics are valuable for research, teaching and knowledge communication. However, the tools used to automate the process are challenging. The purpose of the drawProteins package is to enable the generation of schematics of proteins in an automated fashion that can integrate with the Bioconductor/R suite of tools for bioinformatics and statistical analysis. Using UniProt accession numbers, the package uses the UniProt API to get the features of the protein from the UniProt database. The features are assembled into a data frame and visualized using adaptations of the ggplot2 package. Visualizations can be customised in many ways including adding additional protein features information from other data frames, altering colors and protein names and adding extra layers using other ggplot2 functions. This can be completed within a script that makes the workflow reproducible and sharable. F1000 Research Limited 2018-07-18 /pmc/articles/PMC6107989/ /pubmed/30210791 http://dx.doi.org/10.12688/f1000research.14541.1 Text en Copyright: © 2018 Brennan P http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Software Tool Article Brennan, Paul drawProteins: a Bioconductor/R package for reproducible and programmatic generation of protein schematics |
title | drawProteins: a Bioconductor/R package for reproducible and programmatic generation of protein schematics |
title_full | drawProteins: a Bioconductor/R package for reproducible and programmatic generation of protein schematics |
title_fullStr | drawProteins: a Bioconductor/R package for reproducible and programmatic generation of protein schematics |
title_full_unstemmed | drawProteins: a Bioconductor/R package for reproducible and programmatic generation of protein schematics |
title_short | drawProteins: a Bioconductor/R package for reproducible and programmatic generation of protein schematics |
title_sort | drawproteins: a bioconductor/r package for reproducible and programmatic generation of protein schematics |
topic | Software Tool Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6107989/ https://www.ncbi.nlm.nih.gov/pubmed/30210791 http://dx.doi.org/10.12688/f1000research.14541.1 |
work_keys_str_mv | AT brennanpaul drawproteinsabioconductorrpackageforreproducibleandprogrammaticgenerationofproteinschematics |