Package: procoil 2.35.0

Ulrich Bodenhofer

procoil: Prediction of Oligomerization of Coiled Coil Proteins

The package allows for predicting whether a coiled coil sequence (amino acid sequence plus heptad register) is more likely to form a dimer or more likely to form a trimer. Additionally to the prediction itself, a prediction profile is computed which allows for determining the strengths to which the individual residues are indicative for either class. Prediction profiles can also be visualized as curves or heatmaps.

Authors:Ulrich Bodenhofer [aut,cre]

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procoil.pdf |procoil.html
procoil/json (API)
NEWS

# Install 'procoil' in R:
install.packages('procoil', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/ubod/procoil/issues

Datasets:

On BioConductor:procoil-2.35.0(bioc 3.21)procoil-2.34.0(bioc 3.20)

proteomicsclassificationsupportvectormachine

4.95 score 1 scripts 434 downloads 6 exports 30 dependencies

Last updated 2 months agofrom:57dcf7bb0f. Checks:OK: 5 NOTE: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 01 2024
R-4.5-winNOTEDec 01 2024
R-4.5-linuxNOTEDec 01 2024
R-4.4-winOKDec 01 2024
R-4.4-macOKDec 01 2024
R-4.3-winOKDec 01 2024
R-4.3-macOKDec 01 2024

Exports:heatmapplotpredictreadCCModelshowwriteCCModel

Dependencies:apclusteraskpassBiocGenericsBiostringsclasscrayoncurle1071genericsGenomeInfoDbGenomeInfoDbDatahttrIRangesjsonlitekebabskernlablatticeLiblineaRMASSMatrixmimeopensslproxyR6RcppS4VectorssysUCSC.utilsXVectorzlibbioc

PrOCoil - A Web Service and an R Package for Predicting the Oligomerization of Coiled-Coil Proteins

Rendered fromprocoil.Rnwusingknitr::knitron Dec 01 2024.

Last update: 2024-04-25
Started: 2012-03-26

Readme and manuals

Help Manual

Help pageTopics
Prediction of Oligomerization of Coiled Coil Proteinsprocoil-package procoil
Class "CCModel"CCModel CCModel-class PrOCoilModel PrOCoilModelBA show,CCModel-method show.CCModel weights,CCModel-method weights.CCModel
Reading and writing of coiled coil prediction model from/to filesCCModel-FileOps readCCModel writeCCModel
Class "CCProfile"baselines,CCProfile-method baselines.CCProfile CCProfile CCProfile-class fitted,CCProfile-method fitted.CCProfile heatmap,CCProfile,missing-method heatmap.CCProfile profile,CCProfile-method profile.CCProfile profiles,CCProfile-method profiles.CCProfile sequences,CCProfile-method sequences.CCProfile show,CCProfile-method show.CCProfile [,CCProfile,index,ANY,ANY-method
Plotting prediction profilesplot plot,CCProfile,missing-method plot-methods plot.CCProfile
Predict oligomerization of one or more coiled coil segmentspredict predict,CCModel-method predict-methods predict.CCModel