Package: deepredeff 0.1.2
deepredeff: Deep Learning Prediction of Effectors
A tool that contains trained deep learning models for predicting effector proteins. 'deepredeff' has been trained to identify effector proteins using a set of known experimentally validated effectors from either bacteria, fungi, or oomycetes. Documentation is available via several vignettes, and the paper by Kristianingsih and MacLean (2020) <doi:10.1101/2020.07.08.193250>.
Authors:
deepredeff_0.1.2.tar.gz
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deepredeff_0.1.2.tgz(r-4.5-any)deepredeff_0.1.2.tgz(r-4.4-any)deepredeff_0.1.2.tgz(r-4.3-any)
deepredeff_0.1.2.tar.gz(r-4.5-noble)deepredeff_0.1.2.tar.gz(r-4.4-noble)
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deepredeff.pdf |deepredeff.html✨
deepredeff/json (API)
NEWS
| # Install 'deepredeff' in R: |
| install.packages('deepredeff', repos = c('https://ruthkr.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ruthkr/deepredeff/issues
Last updated 2 years agofrom:2515b42ba6. Checks:9 OK. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Mar 30 2025 |
| R-4.5-win | OK | Mar 30 2025 |
| R-4.5-mac | OK | Mar 30 2025 |
| R-4.5-linux | OK | Feb 28 2025 |
| R-4.4-win | OK | Mar 30 2025 |
| R-4.4-mac | OK | Mar 30 2025 |
| R-4.4-linux | OK | Mar 30 2025 |
| R-4.3-win | OK | Mar 30 2025 |
| R-4.3-mac | OK | Mar 30 2025 |
Exports:%>%aas_to_dfaasset_to_dfencode_integerencode_one_hotfasta_to_dfinstall_tensorflowpredict_effector
Dependencies:ade4askpassbackportsbase64encBiocGenericsBiostringsclicolorspaceconfigcrayoncurldplyrfansifarvergenericsGenomeInfoDbGenomeInfoDbDataggplot2ggthemesgluegtableherehttrIRangesisobandjsonlitekeraslabelinglatticelifecyclemagrittrMASSMatrixmgcvmimemunsellnlmeopensslpillarpixmappkgconfigpngprocessxpspurrrR6rappdirsRColorBrewerRcppRcppArmadilloRcppTOMLreticulaterlangrprojrootrstudioapiS4VectorsscalessegmentedseqinrspstringistringrsystensorflowtfautographtfrunstibbletidyselectUCSC.utilsutf8vctrsviridisLitewhiskerwithrXVectoryamlzeallot
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Convert AAString class to dataframe | aas_to_df |
| Convert AAStringset class to dataframe | aasset_to_df |
| 'deepredeff' package | deepredeff-package deepredeff |
| Integer encoder | encode_integer |
| One-hot encoder | encode_one_hot |
| Weighted ensemble | ensemble_weighted |
| Convert fasta format to dataframe | fasta_to_df |
| Get ensemble methods | get_ensemble_method |
| Install the TensorFlow backend | install_tensorflow |
| Load model | load_model |
| Wildcard Expansion on File Paths | package_glob |
| Plot the results of prediction | plot.tbl_deepredeff |
| Predict effector | predict_effector predict_effector.AAString predict_effector.AAStringSet predict_effector.character predict_effector.data.frame predict_effector.default |
| Prediction mapper helper | prediction_mapper |
| Get the summary of the prediction results | summary.tbl_deepredeff |
