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https://github.com/michbur/ampgram
https://github.com/michbur/ampgram
Last synced: 9 days ago
JSON representation
- Host: GitHub
- URL: https://github.com/michbur/ampgram
- Owner: michbur
- Created: 2020-04-29T18:41:29.000Z (over 4 years ago)
- Default Branch: master
- Last Pushed: 2022-02-28T21:10:49.000Z (over 2 years ago)
- Last Synced: 2023-11-20T11:43:17.849Z (12 months ago)
- Language: R
- Size: 47.9 MB
- Stars: 4
- Watchers: 3
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
[](https://www.mdpi.com/1422-0067/21/12/4310/htm)
[](https://cran.r-project.org/package=AmpGram)
[](https://travis-ci.org/michbur/AmpGram)
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 <- read_txt(system.file("AmpGram/prots.txt", package = "AmpGram"))
predict(AmpGram_model, 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.