peplib: Peptide Library Analysis Methods

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

Author
Andrew White <white.d.andrew@gmail.com>
Date of publication
2013-04-15 10:20:32
Maintainer
Andrew White <white.d.andrew@gmail.com>
License
GPL (>= 2)
Version
1.5.1

View on CRAN

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

Files in this package

peplib
peplib/MD5
peplib/data
peplib/data/blosum62.RData
peplib/data/blosum90.RData
peplib/data/blosum50.RData
peplib/data/defaultBaseMatrix.RData
peplib/data/AMPSequences.RData
peplib/data/AMPSequences.response.RData
peplib/data/TULASequences.RData
peplib/data/SHP2Sequences.RData
peplib/NAMESPACE
peplib/man
peplib/man/AMPSequences.Rd
peplib/man/AMPSequences.response.Rd
peplib/man/classify.Rd
peplib/man/MotifModel-class.Rd
peplib/man/BIC.Rd
peplib/man/MotifModelSet-class.Rd
peplib/man/MetricParams-class.Rd
peplib/man/Sequences.Rd
peplib/man/read.sequences.Rd
peplib/man/simpleDescriptors.Rd
peplib/man/write.sequences.Rd
peplib/man/default.MetricParams.Rd
peplib/man/write.fasta.Rd
peplib/man/read.fasta.Rd
peplib/man/SHP2Sequences.Rd
peplib/man/blosum90.Rd
peplib/man/TULASequences.Rd
peplib/man/Descriptors-class.Rd
peplib/man/blosum50.Rd
peplib/man/aclust.Rd
peplib/man/blosum62.Rd
peplib/man/changeClusterFormat.Rd
peplib/man/defaultBaseMatrix.Rd
peplib/R
peplib/R/sysdata.rda
peplib/R/peplib.R
peplib/tutorial.pdf
peplib/.Rinstignore
peplib/DESCRIPTION