UniprotR
Retrieving Information of Proteins from Uniprot
Science Score: 31.0%
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✓CITATION.cff file
Found CITATION.cff file -
○codemeta.json file
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○.zenodo.json file
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✓DOI references
Found 5 DOI reference(s) in README -
○Academic publication links
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○Committers with academic emails
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (12.3%) to scientific vocabulary
Repository
Retrieving Information of Proteins from Uniprot
Basic Info
- Host: GitHub
- Owner: Proteomicslab57357
- License: gpl-3.0
- Language: R
- Default Branch: master
- Size: 399 KB
Statistics
- Stars: 68
- Watchers: 6
- Forks: 18
- Open Issues: 3
- Releases: 0
Metadata Files
README.md
UniprotR: Retrieving and visualizing protein sequence and functional information from Universal Protein Resource (UniProt knowledgebase)
Installation
R
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
```R 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 ```R
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)
Handy visualization for publications
PlotGOAll(GOObj = GeneOntologyObj, Top = 10, directorypath = getwd(), width = 8, height = 5) ```
Enrichment analysis using KEGG, Reactome of protein list ```R Pathway.Enr(Accessions)
For ready graphs for publications
PlotEnrichedGO(Accs = Accessions, Path = getwd(), theme = "lancet", width = 9, height = 5) PlotEnrichedPathways(Accs = Accessions, Path = "Your local path to save graph", theme = "jama", w = 9, h = 5) ```
Get diseases associated with protein list
R
PathologyObj <- GetPathology_Biotech(Accessions)
Diseases <- Get.diseases(PathologyObj)
Get fasta file for protein list
```R
This feature could be used to create a databse search for MS/MS
GETSeqFastaUniprot(Accessions = Accessions, FileName = "Acclist")
**Protein- Protein interaction using STRING**
R
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: MohmedSoudy2009@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.
Owner
- Name: 57357 Proteomics Lab
- Login: Proteomicslab57357
- Kind: user
- Repositories: 2
- Profile: https://github.com/Proteomicslab57357
Children cancer hospital 57357 proteomics and metabolomics lab
Citation (CITATION)
citHeader("To cite UniprotR in publications use:")
citEntry(
entry = "Article",
title = "UniprotR: Retrieving and visualizing protein sequence and functional information from Universal Protein Resource (UniProt knowledgebase)",
author = "Mohamed Soudy, Ali Mostafa Anwar, Eman Ali Ahmed, Aya Osama, Shahd Ezzeldin, Sebaey Mahgou and Sameh Magdeldin",
journal = "Journal of Proteomics",
volume = "213",
pages = "103613",
year = "2020",
issn = "1874-3919",
doi = "10.1016/j.jprot.2019.103613",
url = "http://www.sciencedirect.com/science/article/pii/S1874391919303859",
textVersion = paste("Soudy, M., Anwar, A.M., Ahmed, E.A., Osama, A., Ezzeldin, S., Mahgoub, S. and Magdeldin, S., 2020. UniprotR: Retrieving and visualizing protein sequence and functional information from Universal Protein Resource (UniProt knowledgebase). Journal of Proteomics, 213, p.103613."
)
)
GitHub Events
Total
- Issues event: 3
- Watch event: 9
- Issue comment event: 1
- Fork event: 1
Last Year
- Issues event: 3
- Watch event: 9
- Issue comment event: 1
- Fork event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Ali Youssef | a****9@g****m | 60 |
| Mohmed Soudy | M****9@g****m | 40 |
| Proteomicslab57357 | 5****7 | 25 |
| richelbilderbeek | r****l@r****l | 2 |
| Proteomicslab57357 | p****7@g****m | 2 |
| Sam | 5****n | 2 |
| MohmedSoudy | m****9@g****m | 2 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 30
- Total pull requests: 10
- Average time to close issues: 4 months
- Average time to close pull requests: 7 days
- Total issue authors: 29
- Total pull request authors: 5
- Average comments per issue: 2.93
- Average comments per pull request: 0.0
- Merged pull requests: 6
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 3
- Pull requests: 0
- Average time to close issues: 8 months
- Average time to close pull requests: N/A
- Issue authors: 3
- Pull request authors: 0
- Average comments per issue: 1.33
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- MattiasErhardsson (2)
- richelbilderbeek (1)
- donumanimae (1)
- amechakra (1)
- biochembryony (1)
- samvgon (1)
- grimmem1 (1)
- maringos (1)
- muecker (1)
- RyanWKW (1)
- ramirobarrantes (1)
- acragin (1)
- goncik (1)
- Somu796 (1)
- sarahgraff (1)
Pull Request Authors
- AliYoussef96 (4)
- MohmedSoudy (3)
- samvgon (2)
- richelbilderbeek (1)
- rahul799 (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
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Total downloads:
- cran 868 last-month
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Total dependent packages: 0
(may contain duplicates) -
Total dependent repositories: 2
(may contain duplicates) - Total versions: 36
- Total maintainers: 1
cran.r-project.org: UniprotR
Retrieving Information of Proteins from Uniprot
- Homepage: https://github.com/Proteomicslab57357/UniprotR
- Documentation: http://cran.r-project.org/web/packages/UniprotR/UniprotR.pdf
- License: GPL-3
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Latest release: 2.5.0
published about 1 year ago
Rankings
Maintainers (1)
conda-forge.org: r-uniprotr
- Homepage: https://github.com/Proteomicslab57357/UniprotR
- License: GPL-3.0-only
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Latest release: 2.2.2
published over 3 years ago