ScISI: In Silico Interactome

Package to create In Silico Interactomes

AuthorTony Chiang <tchiang@fhcrc.org>
Date of publicationNone
MaintainerTony Chiang <tchiang@fhcrc.org>
LicenseLGPL
Version1.46.0

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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