Peptides
An R package to calculate indices and theoretical physicochemical properties of peptides and protein sequences.
Science Score: 23.0%
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○CITATION.cff file
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○.zenodo.json file
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○DOI references
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○Academic publication links
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3 of 12 committers (25.0%) from academic institutions -
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○Scientific vocabulary similarity
Low similarity (10.6%) to scientific vocabulary
Keywords
Repository
An R package to calculate indices and theoretical physicochemical properties of peptides and protein sequences.
Statistics
- Stars: 89
- Watchers: 3
- Forks: 24
- Open Issues: 11
- Releases: 11
Topics
Metadata Files
README.md
Peptides
R package to calculate several physicochemical properties and indices for amino-acid sequences as well as to read and plot 'XVG' output files from the 'GROMACS' molecular dynamics package
Install
This package required R version 1.2.2 or higher. If you are using an older version of R you will be prompted to upgrade when you try to install the package.
The official release of Peptides is available on CRAN. To install from CRAN, use the following command:
install.packages("Peptides", dependencies=TRUE)
If you have devtools installed, install the latest stable version this package directly from GitHub:
library(devtools)
install_github("dosorio/Peptides")
library(Peptides)
Available functions
| Code | Function | | :------------- |:-------------| |aaList| Return a vector with the 20 standard aminoacids in upper case| |aaComp | Compute the amino-acid composition of a protein sequence| |aaDescriptors|Compute 66 descriptors for each amino acid of a protein sequence| |aIndex | Compute the aliphatic index of a protein sequence | |autoCorrelation|Compute the auto-correlation index of a protein sequence| |autoCovariance|Compute the auto-covariance index of a protein sequence| |blosumIndices|Compute the BLOSUM62 derived indices of a protein sequence| |boman | Compute the Boman (Potential Protein Interaction) index | |charge | Compute the theoretical net charge of a protein sequence | |crossCovariance|Compute the cross-covariance index of a protein sequence| |crucianiProperties | Compute the Cruciani properties of a protein sequence | |fasgaiVectors| Compute the FASGAI vectors of a protein sequence | |hmoment | Compute the hydrophobic moment of a protein sequence | |hydrophobicity | Compute the hydrophobicity index of a protein sequence | |instaIndex | Compute the instability index of a protein sequence | |kideraFactors | Compute the Kidera factors of a protein sequence | |lengthpep| Compute the aminoacid length of a protein sequence | |massShift | Compute the mass difference of a protein sequence labelled with stable isotope. | |membpos | Compute theoretically the class of a protein sequence | |mswhimScores|Compute the MS-WHIM scores of a protein sequence| |mw | Compute the molecular weight of a protein sequence | |mz | Compute the mass over charge (m/z) of a protein sequence | |pI | Compute the isoelectic point (pI) of a protein sequence | |plotXVG | Plot time series from GROMACS XVG files | |protFP|Compute the protFP descriptors of a protein sequence| |readXVG | Read XVG files from GROMACS molecular dynamics package | |stScales| Compute the ST-scales of a protein sequence| |tScales| Compute the T-scales of a protein sequence| |vhseScales|Compute the VHSE-scales of a protein sequence| |zScales| Compute the Z-scales of a protein sequence |
Available datasets
| Code | Description | |:----------- |:------------| |AAdata | Properties, scales and indices for the 20 naturally occurring amino acids from various sources | |pepdata | A data frame with 21 physicochemical properties and indices from 100 amino-acid sequences (50 antimicrobial and 50 non antimicrobial) |
Citation
Osorio, D., Rondon-Villarreal, P. & Torres, R. Peptides: A package for data mining of antimicrobial peptides. The R Journal. 7(1), 4–14 (2015).
Owner
- Name: Daniel Osorio
- Login: dosorio
- Kind: user
- Location: Austin, TX
- Company: Boston Children's Hospital
- Website: https://dosorio.github.io/
- Twitter: dcosorioh
- Repositories: 6
- Profile: https://github.com/dosorio
Bioinformatics Scientist
GitHub Events
Total
- Watch event: 7
- Fork event: 1
Last Year
- Watch event: 7
- Fork event: 1
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Daniel Camilo Osorio | d****o@g****m | 254 |
| Daniel Osorio | d****h@u****o | 119 |
| Daniel Osorio | d****h@t****u | 25 |
| Daniel Osorio | d****o | 16 |
| Florian Christoph Sigloch | f****h@m****g | 9 |
| jspaezp | j****p@g****m | 7 |
| Aman Verma | a****l@g****m | 2 |
| richelbilderbeek | r****l@r****l | 2 |
| hongbo-zhu-cn | h****n@g****m | 2 |
| Daniel Osorio | d****o@c****o | 1 |
| J. Sebastian Paez | j****p | 1 |
| Luis Pedro Coelho | l****s@l****g | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 24
- Total pull requests: 29
- Average time to close issues: 4 months
- Average time to close pull requests: 1 day
- Total issue authors: 16
- Total pull request authors: 10
- Average comments per issue: 2.13
- Average comments per pull request: 1.21
- Merged pull requests: 24
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- Stortebecker (5)
- richelbilderbeek (3)
- jckkvs (2)
- dosorio (2)
- cbroeckl (1)
- wevxman (1)
- marceelrf (1)
- GaioTransposon (1)
- buzuddha (1)
- biochemie (1)
- richierocks (1)
- Mycorrhiza94 (1)
- tobimaile (1)
- Arthfael (1)
- francisacquah466 (1)
Pull Request Authors
- dosorio (12)
- Stortebecker (5)
- jspaezp (4)
- richelbilderbeek (2)
- hongbo-zhu-cn (2)
- nograpes (1)
- richierocks (1)
- john-j-miles (1)
- luispedro (1)
- jspmccain (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
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Total downloads:
- cran 1,093 last-month
- Total docker downloads: 39
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Total dependent packages: 6
(may contain duplicates) -
Total dependent repositories: 14
(may contain duplicates) - Total versions: 24
- Total maintainers: 1
cran.r-project.org: Peptides
Calculate Indices and Theoretical Physicochemical Properties of Protein Sequences
- Homepage: https://github.com/dosorio/Peptides/
- Documentation: http://cran.r-project.org/web/packages/Peptides/Peptides.pdf
- License: GPL-2
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Latest release: 2.4.6
published about 2 years ago
Rankings
Maintainers (1)
conda-forge.org: r-peptides
- Homepage: https://github.com/dosorio/Peptides/
- License: GPL-2.0-only
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Latest release: 2.4.4
published over 4 years ago
Rankings
Dependencies
- Rcpp * imports
- testthat >= 2.1.0 suggests