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SLGI (version 1.26.0)
Synthetic Lethal Genetic Interaction
Description
A variety of data files and functions for the analysis of genetic interactions
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1.26.0
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Version
1.26.0
License
Artistic-2.0
Maintainer
Nolwenn Le Meur
Last Published
January 1st, 1970
Functions in SLGI (1.26.0)
Search functions
comemberIn
Retrieve the biological complexes.
Boeke
Incidence matrix of Synthetic Lethal interaction from the Boeke Lab
byComplex
Evaluate protein co-membership within cellular organizational units
congruence
Calculate congruence score between pairs of of genes sharing pattern of synthetic genetic interactions (Ye et al. (2005)).
compare
Compare observed data to expected in permutation models
domainDist
Finds the number of gene sets for each shared domain
AtongFnDomain
The functional domains shared by the tested pairs in Tong et al experiment.
Atong
Systematic genetic analysis with ordered arrays of yeast deletion Tong et. al. (2004).
AtongPair
Data frame the pair of yeast gene tested in Tong et al. 2004.
createSquareMatrix
Create a square matrix
gi2007
Synthetic Genetic Interaction data from Collins et al
dSLAM.GPL1444
dSLAM platform used for Synthetic Lethal screens in the Boeke Lab
getUniquePairs
Find unique pairs from an genetic interaction matrix.
gi2005
Genetic Interaction Data (EMAP) from the yeast early secretory pathway
getInteraction
Count genetic interactions within and between cellular organizational units
getSharedDomains
Find domains shared by a given list of gene names.
essglist
The list of yeast essential genes
getSharedInteraction
Calculate the number of shared synthetic genetic interactions between pairs of genes.
getTestedPairs
Find interacting and non-interacting tested pairs from an genetic interaction matrix.
gi2Interactome
Reduce genetic interactions matrix
hyperG
Hypergeometric test
iSummary
Summarize cellular organizational units sharing genetic interaction
seqMatcherAlign
Functions to do local alignment of two sequences using EMBOSS matcher
modelSLGI
Permutation model for assessing synthetic genetic interactions in cellular organizational units.
normInteraction
Normalize a matrix of biological interactions
SGA
Systematic genetic analysis with ordered arrays of yeast deletion.
SGD.SL
Interaction data from the Saccharomyces Genome Database
sharedBy
Find the gene pairs that share a domain.
plot
Graphical method to represent the result of the modelSLGI .
SDL
The Association matrix for the synthetic dosage lethal screens in Yeast.
topInteraction
Extract interacting biological complexes
twoWayTable
Generate two-way table for genetic interaction data
test2Interact
Summarize genetic interactions within or between cellular organizational units
TFmat
Transcription Factor Binding Affinities
withinComplex
Search for protein co-membership within complexes.
sharedInt
List shared genetic interactions between genes
siResult-class
A class for representing the result of the SLGI graph permutation model.