Package: AmpGram 1.1
AmpGram: Prediction of Antimicrobial Peptides
Predicts antimicrobial peptides using random forests trained on the n-gram encoded peptides (10.3390/ijms21124310). The implemented algorithm can be accessed from both the command line and shiny-based GUI. The AmpGram model is too large for CRAN and it has to be downloaded separately from the repository: <https://github.com/michbur/AmpGramModel>.
Authors:
AmpGram_1.1.tar.gz
AmpGram_1.1.zip(r-4.5)AmpGram_1.1.zip(r-4.4)AmpGram_1.1.zip(r-4.3)
AmpGram_1.1.tgz(r-4.4-any)AmpGram_1.1.tgz(r-4.3-any)
AmpGram_1.1.tar.gz(r-4.5-noble)AmpGram_1.1.tar.gz(r-4.4-noble)
AmpGram_1.1.tgz(r-4.4-emscripten)AmpGram_1.1.tgz(r-4.3-emscripten)
AmpGram.pdf |AmpGram.html✨
AmpGram/json (API)
NEWS
| # Install 'AmpGram' in R: |
| install.packages('AmpGram', repos = c('https://michbur.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/michbur/ampgram/issues
- AmpGram_predictions - Prediction of antimicrobial peptides
Last updated 3 years agofrom:b04c301e15. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 20 2024 |
| R-4.5-win | OK | Aug 20 2024 |
| R-4.5-linux | OK | Aug 20 2024 |
| R-4.4-win | OK | Aug 20 2024 |
| R-4.4-mac | OK | Aug 20 2024 |
| R-4.3-win | OK | Aug 20 2024 |
| R-4.3-mac | OK | Aug 20 2024 |
Exports:AmpGram_guiget_AMPsinstall_AmpGramModelpred2dfread_txt
Dependencies:askpassbase64encbiogrambrewbriobslibcachemcallrclicliprcombinatcommonmarkcpp11crayoncredentialscurldescdevtoolsdiffobjdigestdownlitellipsisentropyevaluatefansifastmapfontawesomefsgertghgitcredsgluegmphighrhtmltoolshtmlwidgetshttpuvhttr2inijquerylibjsonliteknitrlaterlatticelifecyclemagrittrmathjaxrMatrixmemoisemimeminiUIopensslpartitionspbapplypillarpkgbuildpkgconfigpkgdownpkgloadpolynompraiseprettyunitsprocessxprofvispromisespspurrrR6raggrangerrappdirsrbibutilsrcmdcheckRcppRcppEigenRdpackrematch2remotesrlangrmarkdownroxygen2rprojrootrstudioapirversionssasssessioninfosetsshinyslamsourcetoolsstringistringrsyssystemfontstestthattextshapingtibbletinytexurlcheckerusethisutf8vctrswaldowhiskerwithrxfunxml2xopenxtableyamlzip
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Prediction of antimicrobial peptides | AmpGram-package AmpGram |
| AmpGram Graphical User Interface | AmpGram_gui |
| Prediction of antimicrobial peptides | AmpGram_predictions |
| Get putative antimicrobial peptides | get_AMPs |
| Install AmpGramModel package containing model for AMP prediction | install_AmpGramModel |
| Convert predictions to data.frame Return predictions as data.frame | pred2df |
| Predict antimicrobial peptides | predict.ampgram_model |
| Read sequences from .txt file | read_txt |
