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-4.7-any)AmpGram_1.1.zip(r-4.6-any)AmpGram_1.1.zip(r-4.5-any)
AmpGram_1.1.tgz(r-4.6-any)AmpGram_1.1.tgz(r-4.5-any)
AmpGram_1.1.tar.gz(r-4.7-any)AmpGram_1.1.tar.gz(r-4.6-any)
AmpGram_1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
AmpGram/json (API)
| # 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 from:b04c301e15. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 182 | ||
| source / vignettes | OK | 232 | ||
| linux-release-x86_64 | OK | 179 | ||
| macos-release-arm64 | OK | 120 | ||
| macos-oldrel-arm64 | OK | 104 | ||
| windows-devel-x86_64 | OK | 111 | ||
| windows-release-x86_64 | OK | 141 | ||
| windows-oldrel-x86_64 | OK | 100 | ||
| wasm-release | OK | 136 |
Exports:AmpGram_guiget_AMPsinstall_AmpGramModelpred2dfread_txt
Dependencies:askpassbase64encbiogrambrewbriobslibcachemcallrclicliprcombinatcommonmarkcpp11crayoncredentialscurldescdevtoolsdiffobjdigestdownlitellipsisentropyevaluatefansifastmapfontawesomefsgertgitcredsgluegmphighrhtmltoolshtmlwidgetshttpuvhttr2inijquerylibjsonliteknitrlaterlatticelifecyclemagrittrMatrixmemoisemimeminiUIopensslotelpakpartitionspbapplypillarpkgbuildpkgconfigpkgdownpkgloadpolynompraiseprettyunitsprocessxprofvispromisespspurrrR6raggrangerrappdirsrbibutilsrcmdcheckRcppRcppEigenRdpackrlangrmarkdownroxygen2rprojrootrstudioapirversionssasssessioninfosetsshinyslamsourcetoolsstringisyssystemfontstestthattextshapingtibbletinytexurlcheckerusethisutf8vctrswaldowhiskerwithrxfunxml2xopenxtableyamlzip
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 |
