UniprotR: Retrieving and visualizing protein sequence and functional information from Universal Protein Resource (UniProt knowledgebase)
Installation
The package is avilable now online at https://proteomicslab57357.shinyapps.io/UniprotR/
install.packages("UniprotR")Description
Connect to Uniprot to retrieve information about proteins using their accession number such information could be name or taxonomy information,The package provides a powerful data retrieval capabilities in addition to screening visualization tool, and ID conversion tool that helps researchers for analyzing their proteomics data as well as subsequent downstream analysis.
Documentation
For the documentation see: UniprotR Documentation.
Package information
- link to package on CRAN: UniprotR
Usage
Example
library(UniprotR)
#Read Accessions from csv file , Note : Accessions must be in the first column.
Accessions <-GetAccessionList("https://s3.amazonaws.com/csvpastebin/uploads/9571fa356c67a0c7c95e8431799a051a/Accessions.csv")
#Get Taxanomy Information
TaxaObj <- GetNamesTaxa(Accessions)
#Visualize Chromosomes localization
PlotChromosomeInfo(TaxaObj)
#Visualize protein's gene name as Network
PlotGenesNetwork(TaxaObj)Gene ontology of protein list
#Get Gene ontolgy Information
GeneOntologyObj <- GetProteinGOInfo(Accessions)
#Plot Biological process information top 10 go terms
PlotGOBiological(GeneOntologyObj, Top = 10)
#Plot molecular function information top 20 go terms
Plot.GOMolecular(GeneOntologyObj, Top = 20)
#Plot subcellualr localization information
Plot.GOSubCellular(GeneOntologyObj)
#Combine Gene ontology plots into one plot
PlotGoInfo(GeneOntologyObj)Enrichment analysis using KEGG, Reactome of protein list
Pathway.Enr(Accessions)Get diseases associated with protein list
PathologyObj <- GetPathology_Biotech(Accessions)
Diseases <- Get.diseases(PathologyObj)Protein- Protein interaction using STRING
#Get Protein-Protein Interaction within input data
#Path example = "E:/Users/Network.pdf"
GetproteinNetwork(Accessions , Path to save your pdf file) Contribution Guidelines
For bugs and suggestions, the most effective way is by raising an issue on the github issue tracker. Github allows you to classify your issues so that we know if it is a bug report, feature request or feedback to the authors.
Email: Proteomicslab2017@gmail.com
Future plans
- Perform literature overview of given protein list.
Citation
Soudy, Mohamed, Ali Mostafa Anwar, Eman Ali Ahmed, Aya Osama, Shahd Ezzeldin, Sebaey Mahgoub, and Sameh Magdeldin. 2020. “UniprotR: Retrieving and Visualizing Protein Sequence and Functional Information from Universal Protein Resource (UniProt Knowledgebase).” Journal of Proteomics 213 (February). Elsevier B.V. doi:10.1016/j.jprot.2019.103613.
