Entry: Atong
Aliases: Atong tong2004raw
Keywords: datasets
Description: Systematic genetic analysis with ordered arrays of yeast deletion Tong et. al. (2004).
URL: ../../../library/SLGI/html/Atong.html

Entry: AtongFnDomain
Aliases: AtongFnDomain
Keywords: datasets
Description: The functional domains shared by the tested pairs in Tong et al experiment.
URL: ../../../library/SLGI/html/AtongFnDomain.html

Entry: AtongPair
Aliases: AtongPair
Keywords: datasets
Description: Data frame the pair of yeast gene tested in Tong et al. 2004.
URL: ../../../library/SLGI/html/AtongPair.html

Entry: Boeke
Aliases: Boeke2006raw Boeke2006
Keywords: datasets
Description: Incidence matrix of Synthetic Lethal interaction from the Boeke Lab
URL: ../../../library/SLGI/html/Boeke.html

Entry: SDL
Aliases: SDL SLchr
Keywords: datasets
Description: The Association matrix for the synthetic dosage lethal screens in Yeast.
URL: ../../../library/SLGI/html/SDL.html

Entry: SGA
Aliases: SGA SGAraw
Keywords: datasets
Description: Systematic genetic analysis with ordered arrays of yeast deletion.
URL: ../../../library/SLGI/html/SGA.html

Entry: SGD.SL
Aliases: SGD.SL SGD.SynRescue SGD.SynGrowthDefect
Keywords: datasets
Description: Interaction data from the Saccharomyces Genome Database
URL: ../../../library/SLGI/html/SGD.SL.html

Entry: TFmat
Aliases: TFmat
Keywords: datasets
Description: Transcription Factor Binding Affinities
URL: ../../../library/SLGI/html/TFmat.html

Entry: byComplex
Aliases: byComplex
Keywords: data manip
Description: Evaluate protein co-membership within cellular organizational units
URL: ../../../library/SLGI/html/byComplex.html

Entry: comemberIn
Aliases: comemberIn
Keywords: data manip
Description: Retrieve the biological complexes.
URL: ../../../library/SLGI/html/comemberIn.html

Entry: compare
Aliases: compare compare,siResult-method
Keywords: data manip
Description: Compare observed data to expected in permutation models
URL: ../../../library/SLGI/html/compare.html

Entry: congruence
Aliases: congruence
Keywords: methods
Description: Calculate congruence score between pairs of of genes sharing pattern of synthetic genetic interactions (Ye et al. (2005)).
URL: ../../../library/SLGI/html/congruence.html

Entry: createSquareMatrix
Aliases: createSquareMatrix
Keywords: data manip
Description: Create a square matrix
URL: ../../../library/SLGI/html/createSquareMatrix.html

Entry: dSLAM.GPL1444
Aliases: dSLAM.GPL1444 dSLAM
Keywords: datasets
Description: dSLAM platform used for Synthetic Lethal screens in the Boeke Lab
URL: ../../../library/SLGI/html/dSLAM.GPL1444.html

Entry: domainDist
Aliases: domainDist
Keywords: methods
Description: Finds the number of gene sets for each shared domain
URL: ../../../library/SLGI/html/domainDist.html

Entry: essglist
Aliases: essglist
Keywords: datasets
Description: The list of yeast essential genes
URL: ../../../library/SLGI/html/essglist.html

Entry: getFASTAname
Aliases: getFASTAname
Keywords: methods
Description: Obtain sequence name from FASTA object
URL: ../../../library/SLGI/html/getFASTAname.html

Entry: getInteraction
Aliases: getInteraction
Keywords: methods
Description: Count genetic interactions within and between cellular organizational units
URL: ../../../library/SLGI/html/getInteraction.html

Entry: getSharedDomains
Aliases: getSharedDomains
Keywords: methods
Description: Find domains shared by a given list of gene names.
URL: ../../../library/SLGI/html/getSharedDomains.html

Entry: getSharedInteraction
Aliases: getSharedInteraction
Keywords: methods
Description: Calculate the number of shared synthetic genetic interactions between pairs of genes.
URL: ../../../library/SLGI/html/getSharedInteraction.html

Entry: getTestedPairs
Aliases: getTestedPairs
Keywords: methods
Description: Find interacting and non-interacting tested pairs from an genetic interaction matrix.
URL: ../../../library/SLGI/html/getTestedPairs.html

Entry: getUniquePairs
Aliases: getUniquePairs
Keywords: methods
Description: Find unique pairs from an genetic interaction matrix.
URL: ../../../library/SLGI/html/getUniquePairs.html

Entry: gi2005
Aliases: gi2005 gi2005.metadata
Keywords: datasets
Description: Genetic Interaction Data (EMAP) from the yeast early secretory pathway
URL: ../../../library/SLGI/html/gi2005.html

Entry: gi2007
Aliases: gi2007 gi2007.metadata
Keywords: datasets
Description: Synthetic Genetic Interaction data from Collins et al
URL: ../../../library/SLGI/html/gi2007.html

Entry: gi2Interactome
Aliases: gi2Interactome
Keywords: data manip
Description: Reduce genetic interactions matrix
URL: ../../../library/SLGI/html/gi2Interactome.html

Entry: hyperG
Aliases: hyperG
Keywords: data manip
Description: Hypergeometric test
URL: ../../../library/SLGI/html/hyperG.html

Entry: iSummary
Aliases: iSummary
Keywords: data manip
Description: Summarize cellular organizational units sharing genetic interaction
URL: ../../../library/SLGI/html/iSummary.html

Entry: modelSLGI
Aliases: modelSLGI
Keywords: data manip
Description: Permutation model for assessing synthetic genetic interactions in cellular organizational units.
URL: ../../../library/SLGI/html/modelSLGI.html

Entry: normInteraction
Aliases: normInteraction
Keywords: data manip
Description: Normalize a matrix of biological interactions
URL: ../../../library/SLGI/html/normInteraction.html

Entry: plot
Aliases: plot plot,siResult-method plot,siResult,missing-method
Keywords: data manip
Description: Graphical method to represent the result of the modelSLGI .
URL: ../../../library/SLGI/html/plot.html

Entry: seqMatcherAlign
Aliases: seqMatcherAlign getAlignStats
Keywords: methods
Description: Functions to do local alignment of two sequences using EMBOSS matcher
URL: ../../../library/SLGI/html/seqMatcherAlign.html

Entry: sharedBy
Aliases: sharedBy
Keywords: methods
Description: Find the gene pairs that share a domain.
URL: ../../../library/SLGI/html/sharedBy.html

Entry: sharedInt
Aliases: sharedInt
Keywords: data manip
Description: List shared genetic interactions between genes
URL: ../../../library/SLGI/html/sharedInt.html

Entry: siResult-class
Aliases: siResult-class show,siResult-method
Keywords: classes
Description: A class for representing the result of the SLGI graph permutation model.
URL: ../../../library/SLGI/html/siResult-class.html

Entry: test2Interact
Aliases: test2Interact
Keywords: methods
Description: Summarize genetic interactions within or between cellular organizational units
URL: ../../../library/SLGI/html/test2Interact.html

Entry: topInteraction
Aliases: topInteraction
Keywords: data manip
Description: Extract interacting biological complexes
URL: ../../../library/SLGI/html/topInteraction.html

Entry: twoWayTable
Aliases: twoWayTable
Keywords: methods
Description: Generate two-way table for genetic interaction data
URL: ../../../library/SLGI/html/twoWayTable.html

Entry: withinComplex
Aliases: withinComplex
Keywords: data manip
Description: Search for protein co-membership within complexes.
URL: ../../../library/SLGI/html/withinComplex.html
