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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:

source("https://raw.githubusercontent.com/r-lib/remotes/master/install-github.R")$value("michbur/AmpGram")

After installation GUI can be accessed locally:

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:

install_AmpGramModel()

Antimicrobial peptides might be also identified in the batch mode:

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:

install.packages("curl")

Installation from source on Linux requires libcurl. On Debian or Ubuntu use libcurl4-openssl-dev:

sudo apt-get install -y libcurl-dev

On Fedora, CentOS or RHEL use libcurl-devel:

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:

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.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.