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"

Functions

arp23 Man page
arp23G Man page
arp23Orf Man page
arp23Y2HG Man page
calcGraphStats Man page
cfia Man page
cfiaOrf Man page
checkComplex Man page
checkSGN Man page
compareComplex Man page
compBijection Man page
createGODataFrame Man page
createGOMatrix Man page
createMipsDataFrame Man page
createMipsMatrix Man page
createYeastDataObj Man page
dataS Man page
Desc Man page
Desc,yeastData,character-method Man page
eAt Man page
eAt2 Man page
edgeProp Man page
egEBI16112 Man page
expStats Man page
findSubComp Man page
gavin2mergeMG Man page
getAPMSData Man page
getGOInfo Man page
getLocOrfs Man page
getMipsInfo Man page
getURL Man page
getURL,yeastData,character-method Man page
graphSumStats Man page
ho2mergeMGG Man page
ID Man page
ID,yeastData,character-method Man page
JaccardCoef Man page
krogan2mergeMGGH Man page
locScISI Man page
mapping2SysG Man page
mappingsG Man page
maximizeSimilarity Man page
meanDeg Man page
mergeBGMat Man page
mips2go Man page
nAt Man page
nAtMap Man page
nonGenes Man page
nucComp Man page
recCompSize Man page
redundantM Man page
rmByEvi Man page
runAlignment Man page
runCompareComplex Man page
ScISI Man page
ScISI2html Man page
ScISIC Man page
ScISIverified Man page
subCompM Man page
sumStats Man page
unwanted Man page
unWantedComp Man page
xtraGO Man page
xtraGONodes Man page
yeastData Man page
yeastData-class Man page

Files

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.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.