EpitopePrediction: Predict Binding Between Peptides and MHC Molecules

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).

Author
Johannes Textor [aut, cre], Bjoern Peters [aut]
Date of publication
2016-01-20 14:14:20
Maintainer
Johannes Textor <johannes.textor@gmx.de>
License
CC BY-NC-SA 4.0
Version
0.1-2

View on R-Forge

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

Files in this package

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