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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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Detalles Bibliográficos
Autor principal: Brennan, Paul
Formato: Online Artículo Texto
Lenguaje:English
Publicado: F1000 Research Limited 2018
Materias:
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.
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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
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