Package: ampir
Type: Package
Title: Predict Antimicrobial Peptides
Version: 1.1.0
Date: 2021-06-29
Authors@R: c(person("Legana","Fingerhut",
                     email = "legana.fingerhut@my.jcu.edu.au",
                     role = c("aut", "cre"),
                     comment = c(ORCID = "0000-0002-2482-5336")),
             person("Ira","Cooke",
                     email = "ira.cooke@jcu.edu.au",
                     role = c("aut"),
                     comment = c(ORCID = "0000-0001-6520-1397")),
             person("Jinlong","Zhang",
                     email = "jinlongzhang01@gmail.com",
                     role = c("ctb"),
                     comment = c("R/read_faa.R")),
             person("Nan","Xiao",
                     email = "me@nanx.me",
                     role = c("ctb"),
                     comment = c("R/calc_pseudo_comp.R")))
Description: 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) <doi:10.1038/srep42362>. 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 best results it is important to select
        the model that accurately represents your sequence type: for
        full length proteins, it is recommended to use the default
        "precursor" model. The alternative, "mature", model is best
        suited for mature peptide sequences that represent the final
        antimicrobial peptide sequence after post-translational
        processing. For details see Fingerhut et al. (2020)
        <doi:10.1093/bioinformatics/btaa653>. The 'ampir' package is
        also available via a Shiny based GUI at
        <https://ampir.marine-omics.net/>.
URL: https://github.com/Legana/ampir
License: GPL-2
Encoding: UTF-8
Depends: R (>= 3.5.0)
Imports: Peptides, caret (>= 6.0.0), kernlab, Rcpp, parallel
RoxygenNote: 7.1.1
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, e1071
VignetteBuilder: knitr
LinkingTo: Rcpp
Config/testthat/edition: 3
Config/pak/sysreqs: libicu-dev
Repository: https://legana.r-universe.dev
Date/Publication: 2021-06-29 04:15:52 UTC
RemoteUrl: https://github.com/legana/ampir
RemoteRef: HEAD
RemoteSha: 93bcaa2d074d946eac5d66ef8d3640724e68d725
NeedsCompilation: yes
Packaged: 2026-10-17 06:43:52 UTC; root
Author: Legana Fingerhut [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-2482-5336>),
  Ira Cooke [aut] (ORCID: <https://orcid.org/0000-0001-6520-1397>),
  Jinlong Zhang [ctb] (R/read_faa.R),
  Nan Xiao [ctb] (R/calc_pseudo_comp.R)
Maintainer: Legana Fingerhut <legana.fingerhut@my.jcu.edu.au>