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PCpheno (version 1.32.0)
Phenotypes and cellular organizational units
Description
Tools to integrate, annotate, and link phenotypes to cellular organizational units such as protein complexes and pathways.
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1.32.0
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Version
1.32.0
License
Artistic-2.0
Maintainer
Nolwenn Le Meur
Last Published
January 1st, 1970
Functions in PCpheno (1.32.0)
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categoryToEntrezBuilder
Return a list mapping multi-protein complexes IDs to YEAST ids
CoHyperGParams-class
Class "CoHyperGParams"
overlap
Count the number of proteins shared by protein complexes
OsterbergRaw
Data from Osterberg at al. 2006
HI
Data from Deutshbauer et al. (2005)
KEGG2SCISI
Mapping between KEGG and ScISI
gtResult-class
A class for representing the result of a graphTheory test.
LesageRaw
Data from Lesage et al. 2005
GiaeverPheno
List of fitness defect score generated from Giaever et al 2002
graphTheory
Graph theory to test associations between two or more relationships
KastenmayerRaw
Data from Kastenmayer et al. 2006
PCpheno-package
Linkage between Protein Complexes, Pathways, and Phenotypes
truncName
Truncate character strings
testResult-class
A virtual class for representing the result of a test.
SGDphenoL
Saccharomyces Genome Database list of phenotypic data
reduceM
Resize a matrix
YEASTOHNOLOG
List of ohnolog gene pairs from Byrne, K.P and Wolfe, K.H (2005)
densityEstimate
Observed versus Expected Ratios
complexStatus
Complex Status
plot
Graphical method to represent the result of the density or graph test.
ppiInteract
Test the association between AP-MS data and phenotype
getDescr
Get formatted annotation data
DudleyPheno
List of fitness defect score generated from Dudley et al 2005
getFDgene
Get fitness defect genes
buildFDMat
Build fitness defect contingency matrix
CoHyperGResult-class
Class "CoHyperGResult"
deResult-class
A class for representing the result of a densityEstimate test.