API for vitkl/MItools
Molecular interaction data tools, retrieving data using PSICQUIC service

Global functions
ELMdb2GRanges Man page Source code
GGally_d2_bin_log10 Source code
GGally_log10_density Source code
GRangesINinteractionSubsetFASTA Man page Source code
LSFrunQSLIMFinder Man page Source code
MITABregionFeature Man page Source code
NuniqueInteractions Man page Source code
NuniqueInteractors Man page Source code
PPInetwork2SLIMFinder Man page Source code
PermutResult2D Man page Source code
QSLIMFinderCommand Man page Source code
SLIMFinderOcc2GRanges Man page Source code
SubsetByInterProEntryType Source code
XYZ.p.adjust Man page Source code
addInterProEntryTypes Man page Source code
aggregatePermutations Man page Source code
benchmarkMotifs Man page Source code
benchmarkMotifsROC Man page Source code
browseMIontology Man page Source code
calcObservedStatistic Man page Source code
calcPermutedStatistic Man page Source code
centerDomains Man page Source code
checkSelectNodes Man page Source code
checkSelectNodesList Man page Source code
cleanMITAB Man page Source code
cleanMITAB25 Man page Source code
cleanMITAB27 Man page Source code
collapseByInterProID Man page Source code
domainEnrichment Man page Source code
domainProteinPairMatch Man page Source code
downloadFasta Man page Man page Source code
downloadFastaMixed Man page Source code
downloadFastaPostproc Man page Source code
edgelist2degree Man page Source code
edgelist2degreeFreq Man page Source code
edgelist2degree_slow Man page Source code
extractInteractors Man page Source code
filterBYmotifType Man page Source code
filterByFormula Man page Source code
filterByList Man page Source code
filterInteractionSubsetFASTA_list Man page Source code
findOverlapsBench Man page Source code
foldEnrichment Man page Source code
foldEnrichmentDist Man page Source code
foldEnrichmentDist_pasteSplit Source code
foldEnrichmentPval Man page Source code
formula2colnames Man page Source code
formula2nodes Man page Source code
fullInteractome Man page Source code
generateDirName Source code
getInterPro2memberDB Source code
getInterProEntryTypes Source code
getLevelXchildren Source code
groupQSLIMFinderCommand Man page Source code
humanViralDegree Man page Source code
interSpeciesInteractome Man page Source code
interactionSubsetFASTA Man page Source code
interactionSubsetMapID Man page Source code
interactorFeatureTypes Man page Source code
jobsCrashed Man page Source code
lastIntActRelease Man page Source code
listInteractionSubsetFASTA Man page Source code
listReleases Source code
listSingleInteractFromSet2 Man page Source code
loadAllFASTA Man page Source code
loadAllIDProteins Man page Source code
loadBioplex Man page Source code
loadChildrenForLevel Source code
loadHumanViralPPI Man page Source code
loadIntActFTP Man page Source code
loadInterProTree Man page Source code
loadMIontology Man page Source code
loadTaxIDAllLower Man page Source code
loadTaxIDProteins Man page Source code
mBenchmarkMotifs Man page Source code
mBenchmarkMotifsROC Man page Source code
mQSLIMFinderCommand Man page Source code
merge2GRangesmcols Man page Source code
modifyMemoryInBsub Man page Source code
motifVariantClass Man page Source code
node_attr2colnames Man page Source code
observedVSpermuted Man page Source code
parReplicate Man page Source code
permutationPval Man page Source code
permutationPvalHelper Man page
plot.XYZinteration_XZEmpiricalPval Source code
plotEnrichment Man page Source code
plotFoldEnrichmentDist Source code
print.InterProTree Source code
print.RAW_MItab25 Source code
print.RAW_MItab25_fullInteractome Source code
print.RAW_MItab25_interSpeciesInteractome Source code
print.RAW_MItab27 Source code
print.RAW_MItab27_fullInteractome Source code
print.RAW_MItab27_interSpeciesInteractome Source code
print.XYZinteration_XZEmpiricalPval Source code
print.clean_MItab25 Source code
print.clean_MItab25_fullInteractome Source code
print.clean_MItab25_fullInteractome_subset Source code
print.clean_MItab25_interSpeciesInteractome Source code
print.clean_MItab25_interSpeciesInteractome_subset Source code
print.clean_MItab25_randomInteractome Source code
print.clean_MItab25_subset Source code
print.clean_MItab27 Source code
print.clean_MItab27_fullInteractome Source code
print.clean_MItab27_fullInteractome_subset Source code
print.clean_MItab27_interSpeciesInteractome Source code
print.clean_MItab27_interSpeciesInteractome_subset Source code
print.clean_MItab27_subset Source code
print.interaction_subset_from_2_sets Source code
printMotifDomainTable Man page Source code
printSubsetByMethodDetails Source code
printSubsetByPMIDsDetails Source code
queryOCCByMCOL Man page Source code
queryPSICQUIC Man page Source code
queryPSICQUICrlib Man page Source code
randomGRanges Man page Source code
randomInteractome Man page Source code
readInterProGFF3 Man page Source code
readInteractome Man page Source code
readQSLIMFinderMain Man page Source code
readQSLIMFinderOccurence Man page Source code
recodeANDinteractionSubsetFASTA Man page Source code
recodeFASTA Man page Source code
reduceOverlappingGRanges Man page Source code
reduceWithMcols Man page Source code
removeInteractionNoFASTA Man page Source code
removeInteractionObsoleteID Man page Source code
removeSelfLoops Man page Source code
reorderMITAB25 Man page Source code
reorderMITAB27 Man page Source code
runCompariMotif3 Man page Source code
runQSLIMFinder Man page Source code
singleInteractFromSet2 Man page Source code
subset2setsBy1ID Man page Source code
subsetMITABbyID Man page Source code
subsetMITABbyMethod Man page Source code
subsetMITABbyPMIDs Man page Source code
writeInteractionSubsetFASTA_list Man page Source code
writePatternList Man page Source code
vitkl/MItools documentation built on Dec. 12, 2017, 1:41 a.m.