SLGI: Synthetic Lethal Genetic Interaction

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

Author
Nolwenn LeMeur, Zhen Jiang, Ting-Yuan Liu, Jess Mar and Robert Gentleman
Date of publication
None
Maintainer
Nolwenn Le Meur <nlemeur@gmail.com>
License
Artistic-2.0
Version
1.34.0

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