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SLGI (version 1.32.0)
Synthetic Lethal Genetic Interaction
Description
A variety of data files and functions for the analysis of genetic interactions
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Version
Version
1.32.0
1.30.0
1.28.0
1.26.0
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Version
1.32.0
License
Artistic-2.0
Maintainer
Nolwenn Le Meur
Last Published
January 1st, 1970
Functions in SLGI (1.32.0)
Search functions
SGA
Systematic genetic analysis with ordered arrays of yeast deletion.
AtongPair
Data frame the pair of yeast gene tested in Tong et al. 2004.
getSharedDomains
Find domains shared by a given list of gene names.
domainDist
Finds the number of gene sets for each shared domain
normInteraction
Normalize a matrix of biological interactions
seqMatcherAlign
Functions to do local alignment of two sequences using EMBOSS matcher
sharedInt
List shared genetic interactions between genes
sharedBy
Find the gene pairs that share a domain.
TFmat
Transcription Factor Binding Affinities
Atong
Systematic genetic analysis with ordered arrays of yeast deletion Tong et. al. (2004).
siResult-class
A class for representing the result of the SLGI graph permutation model.
comemberIn
Retrieve the biological complexes.
essglist
The list of yeast essential genes
topInteraction
Extract interacting biological complexes
gi2Interactome
Reduce genetic interactions matrix
withinComplex
Search for protein co-membership within complexes.
gi2005
Genetic Interaction Data (EMAP) from the yeast early secretory pathway
test2Interact
Summarize genetic interactions within or between cellular organizational units
twoWayTable
Generate two-way table for genetic interaction data
createSquareMatrix
Create a square matrix
SDL
The Association matrix for the synthetic dosage lethal screens in Yeast.
getSharedInteraction
Calculate the number of shared synthetic genetic interactions between pairs of genes.
iSummary
Summarize cellular organizational units sharing genetic interaction
getInteraction
Count genetic interactions within and between cellular organizational units
AtongFnDomain
The functional domains shared by the tested pairs in Tong et al experiment.
byComplex
Evaluate protein co-membership within cellular organizational units
getTestedPairs
Find interacting and non-interacting tested pairs from an genetic interaction matrix.
plot
Graphical method to represent the result of the modelSLGI .
SGD.SL
Interaction data from the Saccharomyces Genome Database
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
gi2007
Synthetic Genetic Interaction data from Collins et al
Boeke
Incidence matrix of Synthetic Lethal interaction from the Boeke Lab
dSLAM.GPL1444
dSLAM platform used for Synthetic Lethal screens in the Boeke Lab
hyperG
Hypergeometric test
getUniquePairs
Find unique pairs from an genetic interaction matrix.
modelSLGI
Permutation model for assessing synthetic genetic interactions in cellular organizational units.