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peptider
R package for working with peptide libraries
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Version
0.2.2
0.1.7
0.1.6
0.1.5
0.1.4
0.1.3
0.1.2
0.1.1
0.1.0
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Install
install.packages('peptider')
Monthly Downloads
215
Version
0.2.2
License
GPL-3
Issues
0
Pull Requests
0
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0
Repository
https://github.com/heike/peptider
Maintainer
Eric Hare
Last Published
September 16th, 2015
Functions in peptider (0.2.2)
Search functions
genNeighbors_reduced
Calculate neighborhood distribution
generateCustom
Generate peptide and library information for a given scheme
libscheme
Get the specified library scheme
detect
Detection probability in a single library of size N
generateCustomProbs
For a given scheme, generate a dataset with the peptide probabilities
coverage
Coverage as expected number of peptides given all possible peptides
makowski
Diversity index according to Makowski
ppeptide
Probability of detection of a peptide sequence
getChoices
Get the number of peptides that reduce to a particular reduced encoding
codons
Compute the number of codon representations for a (vector of) peptide sequence(s)
generateCustomNei
For a given scheme, generate a dataset with the neighborhood information
BLOSUM80
BLOSUM80 matrix
libBuild
Build peptide library of k-length sequences according to specified scheme
diversity
Diversity according to peptides paper (Sieber)
encodingReduce
Reduce the regular encoding to an easier/faster format
genNeighbors
Calculate neighborhood distribution
getCounts
Get the counts possible for each scheme and k
generateCustomLib
For a given scheme, generate a dataset with the library information
getNeighbors
Find all neighbors of degree one for a set of peptide sequences
schemes
Built-in library schemes for peptider
scheme
Get the specified library scheme definition
getNofNeighbors
Compute the number of neighbor of degree one for a set of peptide sequences
efficiency
Relative efficiency of a library