SLGI: Synthetic Lethal Genetic Interaction

A variety of data files and functions for the analysis of genetic interactions

AuthorNolwenn LeMeur, Zhen Jiang, Ting-Yuan Liu, Jess Mar and Robert Gentleman
Date of publicationNone
MaintainerNolwenn Le Meur <nlemeur@gmail.com>
LicenseArtistic-2.0
Version1.34.0

View on Bioconductor

Man pages

Atong: Systematic genetic analysis with ordered arrays of yeast...

AtongFnDomain: The functional domains shared by the tested pairs in Tong et...

AtongPair: Data frame the pair of yeast gene tested in Tong et al. 2004.

Boeke: Incidence matrix of Synthetic Lethal interaction from the...

byComplex: Evaluate protein co-membership within cellular organizational...

comemberIn: Retrieve the biological complexes.

compare: Compare observed data to expected in permutation models

congruence: Calculate congruence score between pairs of of genes sharing...

createSquareMatrix: Create a square matrix

domainDist: Finds the number of gene sets for each shared domain

dSLAM.GPL1444: dSLAM platform used for Synthetic Lethal screens in the Boeke...

essglist: The list of yeast essential genes

getInteraction: Count genetic interactions within and between cellular...

getSharedDomains: Find domains shared by a given list of gene names.

getSharedInteraction: Calculate the number of shared synthetic genetic interactions...

getTestedPairs: Find interacting and non-interacting tested pairs from an...

getUniquePairs: Find unique pairs from an genetic interaction matrix.

gi2005: Genetic Interaction Data (EMAP) from the yeast early...

gi2007: Synthetic Genetic Interaction data from Collins et al

gi2Interactome: Reduce genetic interactions matrix

hyperG: Hypergeometric test

iSummary: Summarize cellular organizational units sharing genetic...

modelSLGI: Permutation model for assessing synthetic genetic...

normInteraction: Normalize a matrix of biological interactions

plot: Graphical method to represent the result of the modelSLGI .

SDL: The Association matrix for the synthetic dosage lethal...

seqMatcherAlign: Functions to do local alignment of two sequences using EMBOSS...

SGA: Systematic genetic analysis with ordered arrays of yeast...

SGD.SL: Interaction data from the Saccharomyces Genome Database

sharedBy: Find the gene pairs that share a domain.

sharedInt: List shared genetic interactions between genes

siResult-class: A class for representing the result of the SLGI graph...

test2Interact: Summarize genetic interactions within or between cellular...

TFmat: Transcription Factor Binding Affinities

topInteraction: Extract interacting biological complexes

twoWayTable: Generate two-way table for genetic interaction data

withinComplex: Search for protein co-membership within complexes.

Files in this package

SLGI/DESCRIPTION
SLGI/NAMESPACE
SLGI/R
SLGI/R/AllClasses.R SLGI/R/AllGenerics.R SLGI/R/comemberIn.R SLGI/R/congruence-methods.R SLGI/R/createSquareMatrix.R SLGI/R/domainDist.R SLGI/R/getSharedDomains.R SLGI/R/getUniquePairs.R SLGI/R/hyperG.R SLGI/R/interaction-methods.R SLGI/R/normInteraction.R SLGI/R/permutationModels-methods.R SLGI/R/permutationModels.R SLGI/R/seqAlign.R SLGI/R/topInteraction.R SLGI/R/twoWayTable.R SLGI/R/withinComplex.R
SLGI/build
SLGI/build/vignette.rds
SLGI/data
SLGI/data/Atong.rda
SLGI/data/AtongFnDomain.rda
SLGI/data/AtongPair.rda
SLGI/data/Boeke2006.rda
SLGI/data/Boeke2006raw.rda
SLGI/data/SDL.rda
SLGI/data/SGA.rda
SLGI/data/SGAraw.rda
SLGI/data/SGD.SL.rda
SLGI/data/SGD.SynGrowthDefect.rda
SLGI/data/SGD.SynRescue.rda
SLGI/data/SLchr.rda
SLGI/data/TFmat.rda
SLGI/data/dSLAM.GPL1444.rda
SLGI/data/dSLAM.rda
SLGI/data/datalist
SLGI/data/essglist.rda
SLGI/data/gi2005.metadata.rda
SLGI/data/gi2005.rda
SLGI/data/gi2007.metadata.rda
SLGI/data/gi2007.rda
SLGI/data/tong2004raw.RData
SLGI/inst
SLGI/inst/Scripts
SLGI/inst/Scripts/ReadTF.R
SLGI/inst/doc
SLGI/inst/doc/SLGI.R
SLGI/inst/doc/SLGI.Rnw
SLGI/inst/doc/SLGI.pdf
SLGI/inst/extdata
SLGI/inst/extdata/binding_by_gene.tsv
SLGI/inst/extdata/orf_trans.fasta.gz
SLGI/man
SLGI/man/Atong.Rd SLGI/man/AtongFnDomain.Rd SLGI/man/AtongPair.Rd SLGI/man/Boeke.Rd SLGI/man/SDL.Rd SLGI/man/SGA.Rd SLGI/man/SGD.SL.Rd SLGI/man/TFmat.Rd SLGI/man/byComplex.Rd SLGI/man/comemberIn.Rd SLGI/man/compare.Rd SLGI/man/congruence.Rd SLGI/man/createSquareMatrix.Rd SLGI/man/dSLAM.GPL1444.Rd SLGI/man/domainDist.Rd SLGI/man/essglist.Rd SLGI/man/getInteraction.Rd SLGI/man/getSharedDomains.Rd SLGI/man/getSharedInteraction.Rd SLGI/man/getTestedPairs.Rd SLGI/man/getUniquePairs.Rd SLGI/man/gi2005.Rd SLGI/man/gi2007.Rd SLGI/man/gi2Interactome.Rd SLGI/man/hyperG.Rd SLGI/man/iSummary.Rd SLGI/man/modelSLGI.Rd SLGI/man/normInteraction.Rd SLGI/man/plot.Rd SLGI/man/seqMatcherAlign.Rd SLGI/man/sharedBy.Rd SLGI/man/sharedInt.Rd SLGI/man/siResult-class.Rd SLGI/man/test2Interact.Rd SLGI/man/topInteraction.Rd SLGI/man/twoWayTable.Rd SLGI/man/withinComplex.Rd
SLGI/vignettes
SLGI/vignettes/SLGI.Rnw
SLGI/vignettes/SLGI.bib

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