peptider: Evaluation of Diversity in Nucleotide Libraries
Version 0.2.2

Evaluation of diversity in peptide libraries, including NNN, NNB, NNK/S, and 20/20 schemes. Custom encoding schemes can also be defined. Metrics for evaluation include expected coverage, relative efficiency, and the functional diversity of the library. Peptide-level inclusion probabilities are computable for both the native and custom encoding schemes.

AuthorHeike Hofmann [aut], Eric Hare [aut, cre], GGobi Foundation [aut]
Date of publication2015-09-16 10:05:27
MaintainerEric Hare <erichare@iastate.edu>
LicenseGPL-3
Version0.2.2
URL https://github.com/heike/peptider
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("peptider")

Getting started

README.md

Popular man pages

generateCustomNei: For a given scheme, generate a dataset with the neighborhood...
genNeighbors: Calculate neighborhood distribution
getCounts: Get the counts possible for each scheme and k
getNeighbors: Find all neighbors of degree one for a set of peptide...
makowski: Diversity index according to Makowski
scheme: Get the specified library scheme definition
schemes: Built-in library schemes for peptider
See all...

All man pages Function index File listing

Man pages

BLOSUM80: BLOSUM80 matrix
codons: Compute the number of codon representations for a (vector of)...
coverage: Coverage as expected number of peptides given all possible...
detect: Detection probability in a single library of size N
diversity: Diversity according to peptides paper (Sieber)
efficiency: Relative efficiency of a library
encodingReduce: Reduce the regular encoding to an easier/faster format
generateCustom: Generate peptide and library information for a given scheme
generateCustomLib: For a given scheme, generate a dataset with the library...
generateCustomNei: For a given scheme, generate a dataset with the neighborhood...
generateCustomProbs: For a given scheme, generate a dataset with the peptide...
genNeighbors: Calculate neighborhood distribution
genNeighbors_reduced: Calculate neighborhood distribution
getChoices: Get the number of peptides that reduce to a particular...
getCounts: Get the counts possible for each scheme and k
getNeighbors: Find all neighbors of degree one for a set of peptide...
getNofNeighbors: Compute the number of neighbor of degree one for a set of...
libBuild: Build peptide library of k-length sequences according to...
libscheme: Get the specified library scheme
makowski: Diversity index according to Makowski
ppeptide: Probability of detection of a peptide sequence
scheme: Get the specified library scheme definition
schemes: Built-in library schemes for peptider

Functions

BLOSUM80 Man page
codons Man page Source code
codonsOne Source code
coverage Man page Source code
detect Man page Source code
diversity Man page Source code
efficiency Man page Source code
encodingReduce Man page Source code
genNeighbors Man page Source code
genNeighbors_reduced Man page Source code
generateCustom Man page Source code
generateCustomLib Man page Source code
generateCustomNei Man page Source code
generateCustomProbs Man page Source code
getChoices Man page Source code Source code
getCounts Man page Source code
getNeighborOne Source code
getNeighbors Man page Source code
getNofNeighbors Man page Source code
getNofNeighborsOne Source code
libBuild Man page Source code
libscheme Man page Source code
makowski Man page Source code
mult_reduced Source code
ppeptide Man page Source code
scheme Man page Source code
schemes Man page

Files

NAMESPACE
data
data/schemes.rda
data/BLOSUM80.rda
R
R/tabulate.r
R/peptider.r
README.md
MD5
DESCRIPTION
man
man/scheme.Rd
man/BLOSUM80.Rd
man/schemes.Rd
man/diversity.Rd
man/detect.Rd
man/codons.Rd
man/coverage.Rd
man/generateCustomLib.Rd
man/genNeighbors_reduced.Rd
man/encodingReduce.Rd
man/getNeighbors.Rd
man/generateCustom.Rd
man/generateCustomNei.Rd
man/libBuild.Rd
man/generateCustomProbs.Rd
man/libscheme.Rd
man/efficiency.Rd
man/genNeighbors.Rd
man/getChoices.Rd
man/makowski.Rd
man/getNofNeighbors.Rd
man/ppeptide.Rd
man/getCounts.Rd
peptider documentation built on May 19, 2017, 1:48 p.m.

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