Predict Antimicrobial Peptides

A toolkit to predict antimicrobial peptides from protein sequences on a genome-wide scale. It incorporates two support vector machine models ("precursor" and "mature") trained on publicly available antimicrobial peptide data using calculated physico-chemical and compositional sequence properties described in Meher et al. (2017) . In order to support genome-wide analyses, these models are designed to accept any type of protein as input and calculation of compositional properties has been optimised for high-throughput use. For details see Fingerhut et al. 2020 .


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Reference manual

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install.packages("ampir")

1.0.0 by Legana Fingerhut, 5 months ago


https://github.com/Legana/ampir


Browse source code at https://github.com/cran/ampir


Authors: Legana Fingerhut [aut, cre] , Ira Cooke [aut] , Jinlong Zhang [ctb] (R/read_faa.R) , Nan Xiao [ctb] (R/calc_pseudo_comp.R)


Documentation:   PDF Manual  


GPL-2 license


Imports Peptides, caret, kernlab, Rcpp, parallel

Suggests testthat, knitr, rmarkdown, e1071

Linking to Rcpp


See at CRAN