EpitopePrediction: Predict Binding Between Peptides and MHC Molecules
Version 0.1-2

Predicts binding of 9-to 12-mer peptides to MHC class I molecules using the stabilized matrix method. Can predict binding for several alleles from humans (HLA A/B), mice (H-2), chimpanzees (Patr A/B), and rhesus macaques (Mamu A/B).

AuthorJohannes Textor [aut, cre], Bjoern Peters [aut]
Date of publication2016-01-20 14:14:20
MaintainerJohannes Textor <johannes.textor@gmx.de>
LicenseCC BY-NC-SA 4.0
Version0.1-2
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("EpitopePrediction", repos="http://R-Forge.R-project.org")

Getting started

Epitope Prediction Using R

Popular man pages

anchorPositions: Determine Anchor Positions
binders: Find MHC Binders in Protein Sequence
plotBindingMotif: Plot an MHC Binding Motif
smm: Peptide-MHC Binding Prediction
smmMatrix: Get Prediction Matrix
supportedMHCs: Supported MHC Molecules and Peptide Lengths
See all...

All man pages Function index File listing

Man pages

anchorPositions: Determine Anchor Positions
binders: Find MHC Binders in Protein Sequence
plotBindingMotif: Plot an MHC Binding Motif
smm: Peptide-MHC Binding Prediction
smmMatrix: Get Prediction Matrix
supportedMHCs: Supported MHC Molecules and Peptide Lengths

Functions

anchorPositions Man page Source code
binders Man page Source code
plotBindingMotif Man page Source code
smm Man page Source code
smmMatrix Man page Source code
supportedMHCs Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/peptide-mhc.R
build
build/vignette.rds
inst
inst/CITATION
inst/doc
inst/doc/epitope-prediction-using-r.Rmd
inst/doc/epitope-prediction-using-r.html
inst/extdata
inst/extdata/H-2-Db-10.txt
inst/extdata/H-2-Db-11.txt
inst/extdata/H-2-Db-8.txt
inst/extdata/H-2-Db-9.txt
inst/extdata/H-2-Dd-10.txt
inst/extdata/H-2-Kb-10.txt
inst/extdata/H-2-Kb-11.txt
inst/extdata/H-2-Kb-8.txt
inst/extdata/H-2-Kb-9.txt
inst/extdata/H-2-Kd-9.txt
inst/extdata/H-2-Kk-10.txt
inst/extdata/H-2-Kk-11.txt
inst/extdata/H-2-Kk-8.txt
inst/extdata/H-2-Kk-9.txt
inst/extdata/H-2-Ld-12.txt
inst/extdata/H-2-Ld-9.txt
inst/extdata/HLA-A0101-10.txt
inst/extdata/HLA-A0101-9.txt
inst/extdata/HLA-A0201-10.txt
inst/extdata/HLA-A0201-11.txt
inst/extdata/HLA-A0201-8.txt
inst/extdata/HLA-A0201-9.txt
inst/extdata/HLA-A0202-10.txt
inst/extdata/HLA-A0202-11.txt
inst/extdata/HLA-A0202-8.txt
inst/extdata/HLA-A0202-9.txt
inst/extdata/HLA-A0203-10.txt
inst/extdata/HLA-A0203-8.txt
inst/extdata/HLA-A0203-9.txt
inst/extdata/HLA-A0206-10.txt
inst/extdata/HLA-A0206-11.txt
inst/extdata/HLA-A0206-8.txt
inst/extdata/HLA-A0206-9.txt
inst/extdata/HLA-A0211-9.txt
inst/extdata/HLA-A0212-9.txt
inst/extdata/HLA-A0216-9.txt
inst/extdata/HLA-A0219-9.txt
inst/extdata/HLA-A0250-9.txt
inst/extdata/HLA-A0301-10.txt
inst/extdata/HLA-A0301-9.txt
inst/extdata/HLA-A1101-10.txt
inst/extdata/HLA-A1101-9.txt
inst/extdata/HLA-A2301-10.txt
inst/extdata/HLA-A2402-10.txt
inst/extdata/HLA-A2402-9.txt
inst/extdata/HLA-A2403-9.txt
inst/extdata/HLA-A2501-9.txt
inst/extdata/HLA-A2601-10.txt
inst/extdata/HLA-A2601-9.txt
inst/extdata/HLA-A2603-9.txt
inst/extdata/HLA-A2902-10.txt
inst/extdata/HLA-A3001-10.txt
inst/extdata/HLA-A3001-9.txt
inst/extdata/HLA-A3002-10.txt
inst/extdata/HLA-A3002-9.txt
inst/extdata/HLA-A3101-10.txt
inst/extdata/HLA-A3101-9.txt
inst/extdata/HLA-A3201-10.txt
inst/extdata/HLA-A3201-9.txt
inst/extdata/HLA-A3301-10.txt
inst/extdata/HLA-A6801-10.txt
inst/extdata/HLA-A6801-9.txt
inst/extdata/HLA-A6802-10.txt
inst/extdata/HLA-A6802-8.txt
inst/extdata/HLA-A6802-9.txt
inst/extdata/HLA-A6901-9.txt
inst/extdata/HLA-A8001-9.txt
inst/extdata/HLA-B0702-10.txt
inst/extdata/HLA-B0702-8.txt
inst/extdata/HLA-B0702-9.txt
inst/extdata/HLA-B0801-10.txt
inst/extdata/HLA-B0801-9.txt
inst/extdata/HLA-B0802-9.txt
inst/extdata/HLA-B1501-9.txt
inst/extdata/HLA-B1502-9.txt
inst/extdata/HLA-B1503-9.txt
inst/extdata/HLA-B1517-9.txt
inst/extdata/HLA-B1801-10.txt
inst/extdata/HLA-B1801-9.txt
inst/extdata/HLA-B2703-9.txt
inst/extdata/HLA-B2705-10.txt
inst/extdata/HLA-B2705-11.txt
inst/extdata/HLA-B2705-8.txt
inst/extdata/HLA-B2705-9.txt
inst/extdata/HLA-B3501-10.txt
inst/extdata/HLA-B3501-9.txt
inst/extdata/HLA-B3901-9.txt
inst/extdata/HLA-B4002-9.txt
inst/extdata/HLA-B4402-10.txt
inst/extdata/HLA-B4402-9.txt
inst/extdata/HLA-B4403-10.txt
inst/extdata/HLA-B4501-10.txt
inst/extdata/HLA-B4601-9.txt
inst/extdata/HLA-B4801-9.txt
inst/extdata/HLA-B5101-10.txt
inst/extdata/HLA-B5101-9.txt
inst/extdata/HLA-B5301-10.txt
inst/extdata/HLA-B5301-9.txt
inst/extdata/HLA-B5401-10.txt
inst/extdata/HLA-B5401-9.txt
inst/extdata/HLA-B5801-10.txt
inst/extdata/HLA-B5801-9.txt
inst/extdata/HLA-B7301-9.txt
inst/extdata/Mamu-A-01-10.txt
inst/extdata/Mamu-A-01-11.txt
inst/extdata/Mamu-A-01-8.txt
inst/extdata/Mamu-A-01-9.txt
inst/extdata/Mamu-A-02-10.txt
inst/extdata/Mamu-A-02-11.txt
inst/extdata/Mamu-A-02-8.txt
inst/extdata/Mamu-A-02-9.txt
inst/extdata/Mamu-A-11-10.txt
inst/extdata/Mamu-A-11-11.txt
inst/extdata/Mamu-A-11-8.txt
inst/extdata/Mamu-A-2201-10.txt
inst/extdata/Mamu-A-2201-9.txt
inst/extdata/Mamu-A-2601-10.txt
inst/extdata/Mamu-A-2601-9.txt
inst/extdata/Mamu-B-01-10.txt
inst/extdata/Mamu-B-01-11.txt
inst/extdata/Mamu-B-01-8.txt
inst/extdata/Mamu-B-01-9.txt
inst/extdata/Mamu-B-03-10.txt
inst/extdata/Mamu-B-03-11.txt
inst/extdata/Mamu-B-03-8.txt
inst/extdata/Mamu-B-03-9.txt
inst/extdata/Mamu-B-08-10.txt
inst/extdata/Mamu-B-08-11.txt
inst/extdata/Mamu-B-08-8.txt
inst/extdata/Mamu-B-08-9.txt
inst/extdata/Mamu-B-17-10.txt
inst/extdata/Mamu-B-17-11.txt
inst/extdata/Mamu-B-17-9.txt
inst/extdata/Mamu-B-48-9.txt
inst/extdata/Mamu-B-52-9.txt
inst/extdata/Patr-A-0101-10.txt
inst/extdata/Patr-A-0101-9.txt
inst/extdata/Patr-A-0301-10.txt
inst/extdata/Patr-A-0301-9.txt
inst/extdata/Patr-A-0401-10.txt
inst/extdata/Patr-A-0401-9.txt
inst/extdata/Patr-A-0701-10.txt
inst/extdata/Patr-A-0701-9.txt
inst/extdata/Patr-A-0901-10.txt
inst/extdata/Patr-A-0901-11.txt
inst/extdata/Patr-A-0901-9.txt
inst/extdata/Patr-B-0101-10.txt
inst/extdata/Patr-B-0101-11.txt
inst/extdata/Patr-B-0101-9.txt
inst/extdata/Patr-B-1301-10.txt
inst/extdata/Patr-B-1301-9.txt
inst/extdata/Patr-B-2401-10.txt
inst/extdata/Patr-B-2401-9.txt
inst/extdata/model_list.txt
man
man/anchorPositions.Rd
man/binders.Rd
man/plotBindingMotif.Rd
man/smm.Rd
man/smmMatrix.Rd
man/supportedMHCs.Rd
vignettes
vignettes/epitope-prediction-using-r.Rmd
EpitopePrediction documentation built on May 21, 2017, 3:52 a.m.

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