Science Score: 20.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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○DOI references
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✓Academic publication links
Links to: mdpi.com -
✓Committers with academic emails
1 of 4 committers (25.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (14.7%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: michbur
- Language: R
- Default Branch: master
- Size: 47.9 MB
Statistics
- Stars: 4
- Watchers: 3
- Forks: 1
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
Identify antimicrobial peptides
AmpGram identifies antimicrobial peptides using n-gram encoding and random forests. It can be also accessed as a web-based service http://www.smorfland.uni.wroc.pl/shiny/AmpGram/.
Local instance of AmpGram
You can install the latest development version of the package:
R
source("https://raw.githubusercontent.com/r-lib/remotes/master/install-github.R")$value("michbur/AmpGram")
After installation GUI can be accessed locally:
R
library(AmpGram)
AmpGram_gui()
Installing dependency: AmpGramModel
To be able to use AmpGram properly, you should have installed the 'AmpGramModel' package available via GitHub. AmpGramModel contains stacked random forest model and informative n-grams required for prediction of antimicrobial peptides. Due to the large size of a model, it needs to be stored in the external repository, as CRAN do not allow upload of files larger than 5 MB.
You can install AmpGramModel using the install_AmpGramModel function:
R
install_AmpGramModel()
Antimicrobial peptides might be also identified in the batch mode:
```R library(AmpGram) library(AmpGramModel)
if you do not have AmpGramModel use:
install_AmpGramModel()
sequences <- readtxt(system.file("AmpGram/prots.txt", package = "AmpGram")) predict(AmpGrammodel, sequences) ```
Unix/macOS: curl
The curl library is one of the dependencies of the AmpGram package and requires additional, non-R software. If you encounter an error concerning curl, please follow instructions below to install curl (adapted from https://github.com/jeroen/curl).
Binary packages for OS-X or Windows can be installed directly from CRAN:
r
install.packages("curl")
Installation from source on Linux requires libcurl. On Debian or Ubuntu use libcurl4-openssl-dev:
bash
sudo apt-get install -y libcurl-dev
On Fedora, CentOS or RHEL use libcurl-devel:
bash
sudo yum install libcurl-devel
On OS-X libcurl is included with the system so nothing extra is needed. However if you want to build against the most recent version of libcurl, install and force-link curl from homebrew:
bash
brew install curl
brew link --force curl
Note that on OS-X you must recompile the R package from source after force-linking curl, otherwise you get a version conflict with the system version of libcurl.
Owner
- Name: Michał Burdukiewicz
- Login: michbur
- Kind: user
- Location: Białystok, Poland
- Website: biogenies.info
- Twitter: burdukiewicz
- Repositories: 240
- Profile: https://github.com/michbur
GitHub Events
Total
Last Year
Committers
Last synced: 12 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Michał Burdukiewicz | m****z@g****m | 52 |
| Filip Pietluch | f****h@g****m | 10 |
| ksidorczuk | s****7@g****m | 7 |
| DominikRafacz | d****z@s****l | 4 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 12 months ago
All Time
- Total issues: 0
- Total pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Total issue authors: 0
- Total 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
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
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- cran 244 last-month
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 1
- Total maintainers: 1
cran.r-project.org: AmpGram
Prediction of Antimicrobial Peptides
- Homepage: https://github.com/michbur/AmpGram
- Documentation: http://cran.r-project.org/web/packages/AmpGram/AmpGram.pdf
- License: GPL-3
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Latest release: 1.0
published about 6 years ago
Rankings
Maintainers (1)
Dependencies
- R >= 3.5.0 depends
- biogram * imports
- devtools * imports
- pbapply * imports
- ranger * imports
- shiny * imports
- stringi * imports
- DT * suggests
- ggplot2 * suggests
- pander * suggests
- rmarkdown * suggests
- shinythemes * suggests
- spelling * suggests