peplib: Peptide Library Analysis Methods
Version 1.5.1

This package provides a variety of methods for dealing with analysis of peptide library data, including clustering, motif finding, and QSAR model fitting.

Browse man pages Browse package API and functions Browse package files

AuthorAndrew White <white.d.andrew@gmail.com>
Date of publication2013-04-15 10:20:32
MaintainerAndrew White <white.d.andrew@gmail.com>
LicenseGPL (>= 2)
Version1.5.1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("peplib")

Man pages

aclust: aclust
AMPSequences: Antimicrobial peptide sequences
AMPSequences.response: Antimicrobial peptide sequence responses
BIC: Bayesian Information Content
blosum50: BLOSUM 50 substitution matrix
blosum62: BLOSUM 62 substitution matrix
blosum90: BLOSUM 90 substitution matrix
changeClusterFormat: Change cluster format
classify: classify
defaultBaseMatrix: defaultBaseMatrix
default.MetricParams: Default parameters for calculating sequence-sequence...
Descriptors-class: Class "Descriptors"
MetricParams-class: Class "MetricParams"
MotifModel-class: Class "MotifModel"
MotifModelSet-class: Class "MotifModelSet"
read.fasta: Read in sequences in FASTA format
read.sequences: Read sequence file
Sequences: Class "Sequences"
SHP2Sequences: SHP-2_N-SH2 peptide sequences
simpleDescriptors: Function "simpleDescriptors"
TULASequences: TULA-2_Post peptide sequences
write.fasta: Write out the sequences as a FASTA file
write.sequences: Write out the sequences as a sequence file

Functions

AMPSequences Man page
AMPSequences.response Man page
BIC Man page
BIC,MotifModel-method Man page
BIC,MotifModelSet-method Man page
BIC.MotifModel Source code
BIC.MotifModelSet Source code
Descriptors Man page
Descriptors-class Man page
EM.SSOOPS.Linked Source code
EMStep.OOPS Source code
EMStep.SSOOPS Source code
EMStep.ZOOPS Source code
FiveTwoCV.Descriptors Source code
FiveTwoCV.Sequences Source code
FiveTwoCV.default Source code
MetricParams Man page
MetricParams-class Man page
MotifModel Man page
MotifModel-class Man page
MotifModel.motifString Source code
MotifModel.plotFits Source code
MotifModel.plotPositions Source code
MotifModel.plotStartingPosition Source code
MotifModelSet Man page
MotifModelSet-class Man page
ROC Source code
SHP2Sequences Man page
Sequences Man page
Sequences-class Man page
TULASequences Man page
[,Sequences-method Man page
aclust Man page Source code
autocorrelation Source code
blosum50 Man page
blosum62 Man page
blosum90 Man page
changeClusterFormat Man page Source code
classify Man page
classify,MotifModelSet-method Man page
classify.MotifModelSet Source code
createSWeights Source code
decoys Source code
default.MetricParams Man page
defaultBaseMatrix Man page
descriptors Man page Source code
dist,Sequences-method Man page
dist.Sequences Source code
empty.df Source code
empty.matrix Source code
explode Source code
factory.OOPS Source code
factory.SSOOPS Source code
factory.ZOOPS Source code
factory.descriptor Source code
findMinDistElement Source code
logLik,MotifModel-method Man page
logLik,MotifModelSet-method Man page
logLik,OOPS-method Man page
logLik,SSOOPS-method Man page
logLik,ZOOPS-method Man page
logLik.MotifModelSet Source code
logLik.OOPS Source code
logLik.SSOOPS Source code
logLik.ZOOPS Source code
modelStep Source code
motifModel Man page Source code
motifModelSet Man page Source code
motifString Man page
motifString,MotifModel-method Man page
plot,Descriptors-method Man page
plot,MotifModel-method Man page
plot,MotifModelSet-method Man page
plot,Sequences-method Man page
plot.Descriptors Source code
plot.MotifModel Source code
plot.MotifModelSet Source code
plot.Sequences Source code
plotFits Man page
plotFits,MotifModel-method Man page
plotPositions Man page
plotPositions,MotifModel-method Man page
plotStartingPosition Man page
plotStartingPosition,MotifModel-method Man page
predict,MotifModel-method Man page
predict,MotifModelSet-method Man page
predict.MotifModel Source code
predict.MotifModelSet Source code
print,MotifModel-method Man page
print.MotifModel Source code
print.Sequences Source code
processError Source code
rbind,Sequences-method Man page
rbind.Sequences Source code
read.fasta Man page Source code
read.sequences Man page Source code
residuals,MotifModel-method Man page
residuals,MotifModelSet-method Man page
residuals.MotifModel Source code
residuals.MotifModelSet Source code
sHammingDist Source code
sdist Source code
simpleDescriptors Man page Source code
wdist Source code
write.fasta Man page Source code
write.sequences Man page Source code

Files

MD5
data
data/blosum62.RData
data/blosum90.RData
data/blosum50.RData
data/defaultBaseMatrix.RData
data/AMPSequences.RData
data/AMPSequences.response.RData
data/TULASequences.RData
data/SHP2Sequences.RData
NAMESPACE
man
man/AMPSequences.Rd
man/AMPSequences.response.Rd
man/classify.Rd
man/MotifModel-class.Rd
man/BIC.Rd
man/MotifModelSet-class.Rd
man/MetricParams-class.Rd
man/Sequences.Rd
man/read.sequences.Rd
man/simpleDescriptors.Rd
man/write.sequences.Rd
man/default.MetricParams.Rd
man/write.fasta.Rd
man/read.fasta.Rd
man/SHP2Sequences.Rd
man/blosum90.Rd
man/TULASequences.Rd
man/Descriptors-class.Rd
man/blosum50.Rd
man/aclust.Rd
man/blosum62.Rd
man/changeClusterFormat.Rd
man/defaultBaseMatrix.Rd
R
R/sysdata.rda
R/peplib.R
tutorial.pdf
.Rinstignore
DESCRIPTION
peplib documentation built on May 19, 2017, 9:28 p.m.