Package: ampir 1.1.0
ampir: 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) <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/>.
Authors:
ampir_1.1.0.tar.gz
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ampir_1.1.0.tgz(r-4.4-x86_64)ampir_1.1.0.tgz(r-4.4-arm64)ampir_1.1.0.tgz(r-4.3-x86_64)ampir_1.1.0.tgz(r-4.3-arm64)
ampir_1.1.0.tar.gz(r-4.5-noble)ampir_1.1.0.tar.gz(r-4.4-noble)
ampir_1.1.0.tgz(r-4.4-emscripten)ampir_1.1.0.tgz(r-4.3-emscripten)
ampir.pdf |ampir.html✨
ampir/json (API)
NEWS
| # Install 'ampir' in R: |
| install.packages('ampir', repos = c('https://legana.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/legana/ampir/issues
Last updated 3 years agofrom:93bcaa2d07. Checks:OK: 1 NOTE: 6 ERROR: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 24 2024 |
| R-4.5-win-x86_64 | NOTE | Aug 24 2024 |
| R-4.5-linux-x86_64 | NOTE | Aug 24 2024 |
| R-4.4-win-x86_64 | NOTE | Aug 24 2024 |
| R-4.4-mac-x86_64 | NOTE | Aug 24 2024 |
| R-4.4-mac-aarch64 | ERROR | Aug 24 2024 |
| R-4.3-win-x86_64 | NOTE | Aug 24 2024 |
| R-4.3-mac-x86_64 | NOTE | Aug 24 2024 |
| R-4.3-mac-aarch64 | ERROR | Aug 24 2024 |
Exports:calculate_featuresdf_to_faapredict_ampsread_faaremove_nonstandard_aa
Dependencies:caretclasscliclockcodetoolscolorspacecpp11data.tablediagramdigestdplyre1071fansifarverforeachfuturefuture.applygenericsggplot2globalsgluegowergtablehardhatipredisobanditeratorskernlabKernSmoothlabelinglatticelavalifecyclelistenvlubridatemagrittrMASSMatrixmgcvModelMetricsmunsellnlmennetnumDerivparallellyPeptidespillarpkgconfigplyrpROCprodlimprogressrproxypurrrR6RColorBrewerRcpprecipesreshape2rlangrpartscalesshapeSQUAREMstringistringrsurvivaltibbletidyrtidyselecttimechangetimeDatetzdbutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Check protein sequences for non-standard amino acids | aaseq_is_valid |
| Calculate amphiphilicity (or hydrophobic moment) | calc_amphiphilicity |
| Calculate the hydrophobicity | calc_hydrophobicity |
| Calculate the molecular weight | calc_mw |
| Calculate the net charge | calc_net_charge |
| Calculate the isoelectric point (pI) | calc_pI |
| Calculate the pseudo amino acid composition | calc_pseudo_comp |
| Calculate a set of numerical features from protein sequences | calculate_features |
| Determine row breakpoints for dividing a dataset into chunks for parallel processing | chunk_rows |
| Save a dataframe in FASTA format | df_to_faa |
| Predict the antimicrobial peptide probability of a protein | predict_amps |
| Read FASTA amino acids file into a dataframe | read_faa |
| Remove non standard amino acids from protein sequences | remove_nonstandard_aa |
| Remove stop codon at end of sequence | remove_stop_codon |
