ScISI: In Silico Interactome

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Package to create In Silico Interactomes

Author
Tony Chiang <tchiang@fhcrc.org>
Date of publication
None
Maintainer
Tony Chiang <tchiang@fhcrc.org>
License
LGPL
Version
1.46.0

View on Bioconductor

Man pages

arp23
Constituent members of Protein Complex Arp 2/3
arp23G
The graph of arg 2/3
arp23Orf
Constituent members of Protein Complex Arp 2/3
arp23Y2HG
A graph of ARP 2/3 containing only Y2H verified interactions
calcGraphStats
A function to calculate the various summary statistics for...
cfia
Constituent members of Protein Complex Cleavage Factor IA...
cfiaOrf
Constituent members of Protein Complex Cleavage Factor IA...
checkComplex
Function to check a list of protein complexes wrt ScISI
checkSGN
A function to check that the protein names are all systematic...
compareComplex
A function to compare two bipartite graph matrices
compBijection
A recursive function that greedily handles the alignment...
createGODataFrame
A function to create a Dataframe from the GO protein...
createGOMatrix
A function to create the bipartite graph (BG) incidence...
createMipsDataFrame
A function that creates a data frame from the MIPS Data
createMipsMatrix
A function to create the bipartite graph incidence matrix...
createYeastDataObj
Creates an object of class yeastData
dataS
A character matrix containing the source data for the ScISI
Desc-methods
A method to return a description of a protein complex
eAt
An edge attribute data file
eAt2
A file containing edge attributes
edgeProp
A function to estimate the edge proportion of a y2h induced...
egEBI16112
A graph example mapping an IntAct ID to Systematic Gene Names
expStats
A data file containing the experimental statistics
findSubComp
A function that looks for either equality between two...
gavin2mergeMG
A data file containing the pre-merged Gavin to (merged)...
getAPMSData
A function to get the estimated complexes from high...
getGOInfo
A function that parses through the GO database; it agreps for...
getLocOrfs
A function to obtain ORFs for the ScISI
getMipsInfo
A function that reads the downloaded text file from the MIPS...
getURL-methods
A method to return an url location of a protein complex
graphSumStats
An initiation function to generate graph statistics
ho2mergeMGG
A data file containing the pre-merged Ho to the (merged)...
ID-methods
A method to return the ID of a protein complex
JaccardCoef
A function to calculate the Jaccard similarity index between...
krogan2mergeMGGH
A data file containing the pre-merged Krogan to the (merged)...
locScISI
A data file used to estimate the location of the complexes of...
mapping2SysG
A example graph of the mapping from IntAct to Systematic...
mappingsG
A example graph of the mapping from IntAct to Systematic...
maximizeSimilarity
A function compares two bipartite graph matrices and finds...
meanDeg
A function to estimate the population mean nodal degree of a...
mergeBGMat
A function that merges two bipartite graph (BG) incidence...
mips2go
A data file containing the pre-merged GO to the MIPS data
nAt
A file containing node attributes
nAtMap
A file containing node attributes
nonGenes
Genes found in MIPS which are not gene locus names
nucComp
A data file containing the nuclear complexes
recCompSize
A function that records the relative sizes of complex C-i...
redundantM
A matrix of redundant complex summary statistics
rmByEvi
A function that parses through each GO protein complex and...
runAlignment
A function to establish preliminaries for the compBijection...
runCompareComplex
A function that calls all other types of comparison functions
ScISI
The In Silico Interactome for Saccharomyces cerevisiae
ScISI2html
A function that generates an html page for the GO and MIPs...
subCompM
A matrix of sub-complex summary statistics
sumStats
A function to calculate some summary statistics between an...
unwanted
GO terms that are parsed but not protein complexes
unWantedComp
A function to manually remove protein complexes from some in...
xtraGO
A character vector of hand selected GO protein complexes
xtraGONodes
A function to check manually curated GO nodes
yeastData-class
Class "yeastData"

Files in this package

ScISI/DESCRIPTION
ScISI/NAMESPACE
ScISI/R
ScISI/R/JaccardCoef.R
ScISI/R/ScISI2html.R
ScISI/R/calcGraphStats.R
ScISI/R/checkComplex.R
ScISI/R/checkSGN.R
ScISI/R/compBijection.R
ScISI/R/compareComplex.R
ScISI/R/createGODataFrame.R
ScISI/R/createGOMatrix.R
ScISI/R/createMipsDataFrame.R
ScISI/R/createMipsMatrix.R
ScISI/R/createYeastDataObj.R
ScISI/R/edgeProp.R
ScISI/R/findSubComp.R
ScISI/R/getAPMSData.R
ScISI/R/getGOInfo.R
ScISI/R/getLocOrfs.R
ScISI/R/getMipsInfo.R
ScISI/R/graphSumStats.R
ScISI/R/initClasses.R
ScISI/R/maximizeSimilarity.R
ScISI/R/meanDeg.R
ScISI/R/mergeBGMat.R
ScISI/R/recCompSize.R
ScISI/R/rmByEvi.R
ScISI/R/runAlignment.R
ScISI/R/runCompareComplex.R
ScISI/R/sumStats.R
ScISI/R/unWantedComp.R
ScISI/R/xtraGONodes.R
ScISI/build
ScISI/build/vignette.rds
ScISI/data
ScISI/data/ScISI.rda
ScISI/data/ScISIC.rda
ScISI/data/ScISIverified.R
ScISI/data/ScISIverified.rda
ScISI/data/arp23.rda
ScISI/data/arp23G.rda
ScISI/data/arp23Orf.rda
ScISI/data/arp23Y2HG.rda
ScISI/data/cfia.rda
ScISI/data/cfiaOrf.rda
ScISI/data/dataS.rda
ScISI/data/eAt.rda
ScISI/data/eAt2.rda
ScISI/data/egEBI16112.rda
ScISI/data/expStats.rda
ScISI/data/gavin2mergeMG.rda
ScISI/data/ho2mergeMGG.rda
ScISI/data/krogan2mergeMGGH.rda
ScISI/data/locScISI.rda
ScISI/data/mapping2SysG.rda
ScISI/data/mappingsG.rda
ScISI/data/mips2go.rda
ScISI/data/nAt.rda
ScISI/data/nAtMap.rda
ScISI/data/nonGenes.rda
ScISI/data/nucComp.rda
ScISI/data/redundantM.rda
ScISI/data/subCompM.rda
ScISI/data/unwanted.rda
ScISI/data/xtraGO.rda
ScISI/inst
ScISI/inst/Scripts
ScISI/inst/Scripts/C1G.rda
ScISI/inst/Scripts/Comments
ScISI/inst/Scripts/Comments2
ScISI/inst/Scripts/ckCrystStruct.R
ScISI/inst/Scripts/createMipsY2HMatrix.R
ScISI/inst/Scripts/createScISI.R
ScISI/inst/Scripts/createScISIC.R
ScISI/inst/Scripts/creatingScISI.Rnw
ScISI/inst/Scripts/estGavin02.R
ScISI/inst/Scripts/estGavin06.R
ScISI/inst/Scripts/estHo02.R
ScISI/inst/Scripts/estKrogan04.R
ScISI/inst/Scripts/estKrogan06.R
ScISI/inst/Scripts/estimateComp.R
ScISI/inst/Scripts/getLocOrfs.Rnw
ScISI/inst/Scripts/getMipsY2HInfo.R
ScISI/inst/Scripts/graphStatistics.Rnw
ScISI/inst/Scripts/notesMips.R
ScISI/inst/Scripts/notesOtherComps
ScISI/inst/Scripts/sim.R
ScISI/inst/Scripts/test1.R
ScISI/inst/TODO
ScISI/inst/TODO/CrystalStructures
ScISI/inst/TODO/Validate
ScISI/inst/doc
ScISI/inst/doc/vignette.R
ScISI/inst/doc/vignette.Rnw
ScISI/inst/doc/vignette.pdf
ScISI/inst/extdata
ScISI/inst/extdata/Arp2_3_complex.jpg
ScISI/inst/extdata/Arp2_3_complex.png
ScISI/inst/extdata/PPI_141105.tab.gz
ScISI/inst/extdata/complexcat.scheme
ScISI/inst/extdata/complexcat.scheme.edit
ScISI/inst/extdata/complexcat_data_14112005.gz
ScISI/inst/extdata/complexcat_data_18052006.gz
ScISI/inst/extdata/complexcat_data_20062005.gz
ScISI/inst/extdata/evidencecat.scheme
ScISI/inst/extdata/graphs
ScISI/inst/extdata/graphs/Readme
ScISI/inst/extdata/graphs/arp23AM.rda
ScISI/inst/extdata/graphs/arp23BP.rda
ScISI/inst/extdata/graphs/arp23BPG.rda
ScISI/inst/extdata/graphs/arp23CMG.rda
ScISI/inst/extdata/graphs/arp23CMM.rda
ScISI/inst/extdata/graphs/arp23G.rda
ScISI/inst/extdata/graphs/cfiaAM.rda
ScISI/inst/extdata/graphs/cfiaCMG.rda
ScISI/inst/extdata/graphs/cfiaCMM.rda
ScISI/inst/extdata/graphs/cfiaG.rda
ScISI/inst/extdata/graphs/ppi1.rda
ScISI/inst/extdata/graphs/ppi1G.rda
ScISI/inst/extdata/graphs/ppi2.rda
ScISI/inst/extdata/graphs/ppi2G.rda
ScISI/inst/extdata/localization
ScISI/inst/extdata/localization/allOrfData.txt
ScISI/inst/extdata/pathway
ScISI/inst/extdata/pathway/biochemical_pathways.tab
ScISI/inst/extdata/pathway/keggM.rda
ScISI/inst/extdata/pathway/sgdPathM.rda
ScISI/inst/extdata/protein_network_large.jpg
ScISI/man
ScISI/man/Desc-methods.Rd
ScISI/man/ID-methods.Rd
ScISI/man/JaccardCoef.Rd
ScISI/man/ScISI.Rd
ScISI/man/ScISI2html.Rd
ScISI/man/arp23.Rd
ScISI/man/arp23G.Rd
ScISI/man/arp23Orf.Rd
ScISI/man/arp23Y2HG.Rd
ScISI/man/calcGraphStats.Rd
ScISI/man/cfia.Rd
ScISI/man/cfiaOrf.Rd
ScISI/man/checkComplex.Rd
ScISI/man/checkSGN.Rd
ScISI/man/compBijection.Rd
ScISI/man/compareComplex.Rd
ScISI/man/createGODataFrame.Rd
ScISI/man/createGOMatrix.Rd
ScISI/man/createMipsDataFrame.Rd
ScISI/man/createMipsMatrix.Rd
ScISI/man/createYeastDataObj.Rd
ScISI/man/dataS.Rd
ScISI/man/eAt.Rd
ScISI/man/eAt2.Rd
ScISI/man/edgeProp.Rd
ScISI/man/egEBI16112.Rd
ScISI/man/expStats.Rd
ScISI/man/findSubComp.Rd
ScISI/man/gavin2mergeMG.Rd
ScISI/man/getAPMSData.Rd
ScISI/man/getGOInfo.Rd
ScISI/man/getLocOrfs.Rd
ScISI/man/getMipsInfo.Rd
ScISI/man/getURL-methods.Rd
ScISI/man/graphSumStats.Rd
ScISI/man/ho2mergeMGG.Rd
ScISI/man/krogan2mergeMGGH.Rd
ScISI/man/locScISI.Rd
ScISI/man/mapping2SysG.Rd
ScISI/man/mappingsG.Rd
ScISI/man/maximizeSimilarity.Rd
ScISI/man/meanDeg.Rd
ScISI/man/mergeBGMat.Rd
ScISI/man/mips2go.Rd
ScISI/man/nAt.Rd
ScISI/man/nAtMap.Rd
ScISI/man/nonGenes.Rd
ScISI/man/nucComp.Rd
ScISI/man/recCompSize.Rd
ScISI/man/redundantM.Rd
ScISI/man/rmByEvi.Rd
ScISI/man/runAlignment.Rd
ScISI/man/runCompareComplex.Rd
ScISI/man/subCompM.Rd
ScISI/man/sumStats.Rd
ScISI/man/unWantedComp.Rd
ScISI/man/unwanted.Rd
ScISI/man/xtraGO.Rd
ScISI/man/xtraGONodes.Rd
ScISI/man/yeastData-class.Rd
ScISI/vignettes
ScISI/vignettes/bioc.bib
ScISI/vignettes/vignette.Rnw