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:Ruth Kristianingsih [aut, cre, cph]

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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'))

Peer review:

Bug tracker:https://github.com/ruthkr/deepredeff/issues

On CRAN:

4.86 score 4 stars 18 scripts 185 downloads 1 mentions 8 exports 78 dependencies

Last updated 1 years agofrom:2515b42ba6. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-winOKOct 31 2024
R-4.5-linuxOKOct 31 2024
R-4.4-winOKOct 31 2024
R-4.4-macOKOct 31 2024
R-4.3-winOKOct 31 2024
R-4.3-macOKOct 31 2024

Exports:%>%aas_to_dfaasset_to_dfencode_integerencode_one_hotfasta_to_dfinstall_tensorflowpredict_effector

Dependencies:ade4askpassbackportsbase64encBiocGenericsBiostringsclicolorspaceconfigcrayoncurldplyrfansifarvergenericsGenomeInfoDbGenomeInfoDbDataggplot2ggthemesgluegtableherehttrIRangesisobandjsonlitekeraslabelinglatticelifecyclemagrittrMASSMatrixmgcvmimemunsellnlmeopensslpillarpixmappkgconfigpngprocessxpspurrrR6rappdirsRColorBrewerRcppRcppArmadilloRcppTOMLreticulaterlangrprojrootrstudioapiS4VectorsscalessegmentedseqinrspstringistringrsystensorflowtfautographtfrunstibbletidyselectUCSC.utilsutf8vctrsviridisLitewhiskerwithrXVectoryamlzeallotzlibbioc

General overview of deepredeff

Rendered fromoverview.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2023-09-14
Started: 2020-06-25

More in predicting sequences

Rendered frompredict.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2020-07-08
Started: 2020-05-19

Readme and manuals

Help Manual

Help pageTopics
Convert AAString class to dataframeaas_to_df
Convert AAStringset class to dataframeaasset_to_df
'deepredeff' packagedeepredeff-package deepredeff
Integer encoderencode_integer
One-hot encoderencode_one_hot
Weighted ensembleensemble_weighted
Convert fasta format to dataframefasta_to_df
Get ensemble methodsget_ensemble_method
Install the TensorFlow backendinstall_tensorflow
Load modelload_model
Wildcard Expansion on File Pathspackage_glob
Plot the results of predictionplot.tbl_deepredeff
Predict effectorpredict_effector predict_effector.AAString predict_effector.AAStringSet predict_effector.character predict_effector.data.frame predict_effector.default
Prediction mapper helperprediction_mapper
Get the summary of the prediction resultssummary.tbl_deepredeff