SLGI: Synthetic Lethal Genetic Interaction

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

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("SLGI")
AuthorNolwenn LeMeur, Zhen Jiang, Ting-Yuan Liu, Jess Mar and Robert Gentleman
Bioconductor views Genetics GraphAndNetwork Network Proteomics
Date of publicationNone
MaintainerNolwenn Le Meur <nlemeur@gmail.com>
LicenseArtistic-2.0
Version1.36.0

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.

Functions

Atong Man page
AtongFnDomain Man page
AtongPair Man page
Boeke2006 Man page
Boeke2006raw Man page
byComplex Man page
comemberIn Man page
compare Man page
compare,siResult-method Man page
congruence Man page
createSquareMatrix Man page
domainDist Man page
dSLAM Man page
dSLAM.GPL1444 Man page
essglist Man page
getAlignStats Man page
getInteraction Man page
getSharedDomains Man page
getSharedInteraction Man page
getTestedPairs Man page
getUniquePairs Man page
gi2005 Man page
gi2005.metadata Man page
gi2007 Man page
gi2007.metadata Man page
gi2Interactome Man page
hyperG Man page
iSummary Man page
modelSLGI Man page
normInteraction Man page
plot Man page
plot,siResult-method Man page
plot,siResult,missing-method Man page
SDL Man page
seqMatcherAlign Man page
SGA Man page
SGAraw Man page
SGD.SL Man page
SGD.SynGrowthDefect Man page
SGD.SynRescue Man page
sharedBy Man page
sharedInt Man page
show,siResult-method Man page
siResult-class Man page
SLchr Man page
test2Interact Man page
TFmat Man page
tong2004raw Man page
topInteraction Man page
twoWayTable Man page
withinComplex Man page

Files

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

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