Comprior
latest
Contents:
Installation and Usage
Example Use Cases
Input Data Sets
Configuration Parameters
Folder Structure - Where to find what Files (In- and Output)
Knowledge Bases
Prior Knowledge Approaches
Extending Comprior - How-Tos
Python Code Documentation
R Code Documentation
Java Code Documentation
System Architecture
Comprior
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B
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C
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D
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E
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F
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G
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H
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I
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J
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K
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
A
addlist() (knowledgebases.ENRICHR method)
Analyzer (Java class)
Analyzer(Instances) (Java constructor)
annotateGene() (knowledgebases.Enrichr method)
annotateGenes() (knowledgebases.Enrichr method)
AnnotationEvaluator (class in evaluation)
AnovaSelector (class in featureselection)
assignColors() (pipeline.Pipeline method)
assignMarkers() (pipeline.Pipeline method)
AttributeRemover (class in evaluation)
AttributeSelector (Java class)
AttributeSelector(Instances, String) (Java constructor)
B
benchutils (module)
BioMART (class in knowledgebases)
C
checkCoverage() (evaluation.KnowledgeBaseEvaluator method)
checkPathwayCoverage() (evaluation.KnowledgeBaseEvaluator method)
ClassificationEvaluator (class in evaluation)
classifyAndEvaluate(String, String, String, int, int, int, String[], String[]) (Java method)
cleanupResults() (in module benchutils)
collectAlternativeSearchTerms() (featureselection.PriorKnowledgeSelector method)
combineRankings() (featureselection.KBweightedSelector method)
CombiningSelector (class in featureselection)
computeActivityScore() (featureselection.CORGSActivityMapper method)
computeActivityVector() (featureselection.CORGSActivityMapper method)
computeExternalRankings() (featureselection.KBweightedSelector method)
(featureselection.LassoPenalty method)
computeFoldChangeDiffs() (evaluation.RankingsEvaluator method)
computeGeneVariances() (featureselection.PathwayActivityMapper method)
computeKendallsW() (evaluation.Evaluator method)
computeKendallsWScores() (evaluation.RankingsEvaluator method)
computeOverlap() (evaluation.AnnotationEvaluator method)
computePValue() (evaluation.RankingsEvaluator method)
computeStatisticalRankings() (featureselection.KBweightedSelector method)
CORGSActivityMapper (class in featureselection)
countAnnotationPercentages() (evaluation.AnnotationEvaluator method)
createClassifier() (featureselection.WrapperSelector method)
createDirectory() (in module benchutils)
createKnowledgeBases() (evaluation.KnowledgeBaseEvaluator method)
createLogger() (in module benchutils)
createOrClearDirectory() (in module benchutils)
createParams() (featureselection.InfoGainSelector method)
(featureselection.JavaSelector method)
(featureselection.LassoPenalty method)
(featureselection.MRMRSelector method)
(featureselection.RSelector method)
(featureselection.ReliefFSelector method)
(featureselection.SVMRFESelector method)
(featureselection.VarianceSelector method)
createSelector() (featureselection.WrapperSelector method)
createTimeLog() (in module benchutils)
CrossEvaluator (class in evaluation)
D
data (Java field)
DataCharacteristicsPlotting.R (directive)
DataLoader (Java class)
DataLoader(String, String) (Java constructor)
DataMovePreprocessor (class in preprocessing)
DatasetEvaluator (class in evaluation)
DataTransformationPreprocessor (class in preprocessing)
de.hpi.bmg (package)
default_extension (knowledgebases.PATHWAYCOMMONSWS attribute)
disableLogFlush() (featureselection.FeatureSelector method)
DISGENET (class in knowledgebases)
Disgenet (class in knowledgebases)
downloadEnrichedTerms() (knowledgebases.Enrichr method)
drawBoxPlot() (evaluation.RankingsEvaluator method)
drawCombinedPlot() (evaluation.KnowledgeBaseEvaluator method)
drawLinePlot() (evaluation.ClassificationEvaluator method)
E
enableLogFlush() (featureselection.FeatureSelector method)
enrich() (knowledgebases.ENRICHR method)
enrichGeneset() (knowledgebases.Enrichr method)
ENRICHR (class in knowledgebases)
Enrichr (class in knowledgebases)
evaluate() (evaluation.AnnotationEvaluator method)
(evaluation.ClassificationEvaluator method)
(evaluation.CrossEvaluator method)
(evaluation.DatasetEvaluator method)
(evaluation.Evaluator method)
(evaluation.KnowledgeBaseEvaluator method)
(evaluation.RankingsEvaluator method)
evaluateBiomarkers() (pipeline.Pipeline method)
evaluateInputData() (pipeline.Pipeline method)
evaluateKnowledgeBases() (pipeline.Pipeline method)
evaluation (module)
Evaluator (class in evaluation)
executePipeline() (pipeline.Pipeline method)
export() (knowledgebases.ENRICHR method)
ExtensionSelector (class in featureselection)
F
FeatureMapper (class in featureselection)
featureselection (module)
FeatureSelector (class in featureselection)
FeatureSelectorFactory (class in featureselection)
filterMissings() (preprocessing.FilterPreprocessor method)
filterPathways() (featureselection.NetworkSelector method)
FilterPreprocessor (class in preprocessing)
flushTimeLog() (in module benchutils)
FS_LassoPenalty.R (directive)
FS_mRMR.R (directive)
FS_Variance.R (directive)
G
GCONVERT (class in knowledgebases)
Gconvert (class in knowledgebases)
genemap() (knowledgebases.ENRICHR method)
generateOverlaps() (evaluation.RankingsEvaluator method)
get() (knowledgebases.PATHWAYCOMMONSWS method)
getANOVAscores() (featureselection.CORGSActivityMapper method)
getAssociations() (knowledgebases.OpenTargets method)
getAverageCorrelation() (featureselection.PathwayActivityMapper method)
getConfig() (in module benchutils)
getConfigBoolean() (in module benchutils)
getConfigValue() (in module benchutils)
getCUIs() (knowledgebases.UMLS method)
getData() (featureselection.FeatureSelector method)
(Java method)
getExternalGenes() (featureselection.CombiningSelector method)
getFeatures() (featureselection.FeatureMapper method)
(featureselection.FeatureSelector method)
getGeneScores() (knowledgebases.BioMART method)
(knowledgebases.Disgenet method)
(knowledgebases.Enrichr method)
(knowledgebases.Gconvert method)
(knowledgebases.Kegg method)
(knowledgebases.KnowledgeBase method)
(knowledgebases.OpenTargets method)
(knowledgebases.Pathwaycommons method)
getLabels() (featureselection.FeatureMapper method)
(featureselection.FeatureSelector method)
getName() (featureselection.CombiningSelector method)
(featureselection.FeatureSelector method)
(featureselection.KBweightedSelector method)
(featureselection.LassoPenalty method)
(featureselection.NetworkSelector method)
(featureselection.PriorKnowledgeSelector method)
(knowledgebases.KnowledgeBase method)
getPathwayGenes() (featureselection.FeatureMapper method)
getPathwayNames() (knowledgebases.Kegg method)
getRelevantGenes() (knowledgebases.BioMART method)
(knowledgebases.Disgenet method)
(knowledgebases.Enrichr method)
(knowledgebases.Gconvert method)
(knowledgebases.Kegg method)
(knowledgebases.KnowledgeBase method)
(knowledgebases.OpenTargets method)
(knowledgebases.Pathwaycommons method)
getRelevantPathways() (knowledgebases.BioMART method)
(knowledgebases.Disgenet method)
(knowledgebases.Enrichr method)
(knowledgebases.Gconvert method)
(knowledgebases.Kegg method)
(knowledgebases.KnowledgeBase method)
(knowledgebases.OpenTargets method)
(knowledgebases.Pathwaycommons method)
getSamples() (featureselection.FeatureMapper method)
getSearchTerms() (featureselection.PriorKnowledgeSelector method)
getTimeLogs() (featureselection.FeatureSelector method)
getUniqueLabels() (featureselection.FeatureSelector method)
getUnlabeledData() (featureselection.FeatureMapper method)
(featureselection.FeatureSelector method)
getVersion() (knowledgebases.DISGENET method)
(knowledgebases.PATHWAYCOMMONSWS method)
H
hasGenes() (knowledgebases.KnowledgeBase method)
hasPathways() (knowledgebases.KnowledgeBase method)
I
IdentifierMapping.R (directive)
InfoGainSelector (class in featureselection)
instance (featureselection.FeatureSelectorFactory attribute)
(knowledgebases.KnowledgeBaseFactory attribute)
(knowledgebases.UMLS_AUTH attribute)
J
JavaSelector (class in featureselection)
K
KbSelector (class in featureselection)
KBweightedSelector (class in featureselection)
Kegg (class in knowledgebases)
KEGGPathwayParser (class in knowledgebases)
KnowledgeBase (class in knowledgebases)
KnowledgeBaseEvaluator (class in evaluation)
KnowledgeBaseFactory (class in knowledgebases)
knowledgebases (module)
L
LassoPenalty (class in featureselection)
LassoSelector (class in featureselection)
loadAnnotationFiles() (evaluation.AnnotationEvaluator method)
loadConfig() (in module benchutils)
(pipeline.Pipeline method)
loadData(String) (Java method)
loadGeneRanks() (evaluation.RankingsEvaluator method)
loadRanking() (in module benchutils)
loadRankings() (evaluation.Evaluator method)
loadTopKRankings() (evaluation.AttributeRemover method)
logDebug() (in module benchutils)
logError() (in module benchutils)
logInfo() (in module benchutils)
logRuntime() (in module benchutils)
logWarning() (in module benchutils)
M
main(String[]) (Java method)
,
[1]
mapDataMatrix() (in module benchutils)
mapFeatures() (featureselection.CORGSActivityMapper method)
(featureselection.FeatureMapper method)
(featureselection.PathwayActivityMapper method)
mapGeneList() (in module benchutils)
mapIdentifiers() (in module benchutils)
mapItems() (knowledgebases.BioMART method)
(knowledgebases.Gconvert method)
MappingPreprocessor (class in preprocessing)
mapRanking() (in module benchutils)
MetaDataPreprocessor (class in preprocessing)
MRMRSelector (class in featureselection)
N
NetworkActivitySelector (class in featureselection)
NetworkSelector (class in featureselection)
O
OpenTargets (class in knowledgebases)
P
parsePathway() (knowledgebases.KEGGPathwayParser method)
(knowledgebases.PathwayParser method)
PathwayActivityMapper (class in featureselection)
Pathwaycommons (class in knowledgebases)
PATHWAYCOMMONSWS (class in knowledgebases)
PathwayParser (class in knowledgebases)
Pipeline (class in pipeline)
pipeline (module)
PostFilterSelector (class in featureselection)
PreFilterSelector (class in featureselection)
prepareDirectories() (pipeline.Pipeline method)
prepareExecution() (pipeline.Pipeline method)
prepareInput() (featureselection.PythonSelector method)
prepareOutput() (featureselection.LassoSelector method)
(featureselection.PythonSelector method)
(featureselection.RandomForestSelector method)
(featureselection.Variance2Selector method)
(featureselection.WrapperSelector method)
preprocess() (preprocessing.DataMovePreprocessor method)
(preprocessing.DataTransformationPreprocessor method)
(preprocessing.FilterPreprocessor method)
(preprocessing.MappingPreprocessor method)
(preprocessing.MetaDataPreprocessor method)
(preprocessing.Preprocessor method)
preprocessData() (pipeline.Pipeline method)
preprocessing (module)
Preprocessor (class in preprocessing)
PriorKnowledgeSelector (class in featureselection)
PythonSelector (class in featureselection)
Q
query() (knowledgebases.DISGENET method)
(knowledgebases.GCONVERT method)
R
RandomForestSelector (class in featureselection)
RandomSelector (class in featureselection)
RankingsEvaluator (class in evaluation)
readInteractions() (knowledgebases.KEGGPathwayParser method)
readPathway() (knowledgebases.Pathwaycommons method)
ReliefFSelector (class in featureselection)
removeAttributesFromDataset() (evaluation.AttributeRemover method)
removeDirectoryContent() (in module benchutils)
removeFile() (in module benchutils)
removeUnusedAttributes() (evaluation.AttributeRemover method)
retrieveMappings() (in module benchutils)
RSelector (class in featureselection)
runFeatureSelector() (pipeline.Pipeline method)
runJavaCommand() (in module benchutils)
runRCommand() (in module benchutils)
runSelector() (featureselection.AnovaSelector method)
(featureselection.LassoSelector method)
(featureselection.PythonSelector method)
(featureselection.RandomForestSelector method)
(featureselection.Variance2Selector method)
(featureselection.WrapperSelector method)
S
saveSelectedAttributes(String) (Java method)
search() (knowledgebases.PATHWAYCOMMONSWS method)
selectAttributes() (Java method)
selectFeatures() (featureselection.CombiningSelector method)
(featureselection.ExtensionSelector method)
(featureselection.FeatureSelector method)
(featureselection.JavaSelector method)
(featureselection.KBweightedSelector method)
(featureselection.KbSelector method)
(featureselection.LassoPenalty method)
(featureselection.NetworkSelector method)
(featureselection.PostFilterSelector method)
(featureselection.PreFilterSelector method)
(featureselection.PriorKnowledgeSelector method)
(featureselection.PythonSelector method)
(featureselection.RSelector method)
(featureselection.RandomSelector method)
(pipeline.Pipeline method)
selectPathways() (featureselection.NetworkActivitySelector method)
(featureselection.NetworkSelector method)
setParams() (featureselection.FeatureSelector method)
setTimeLogs() (featureselection.FeatureSelector method)
sourceFile (Java field)
suppress_stdout() (in module knowledgebases)
SVMRFESelector (class in featureselection)
T
trainAndEvaluateWithTopKAttributes(int, int, AbstractClassifier[], String[]) (Java method)
U
UMLS (class in knowledgebases)
UMLS_AUTH (class in knowledgebases)
updateScores() (featureselection.KbSelector method)
(featureselection.KBweightedSelector method)
UpsetDiagramCreation.R (directive)
V
Variance2Selector (class in featureselection)
VarianceSelector (class in featureselection)
W
WEKA_Evaluator (Java class)
WEKA_FeatureSelector (Java class)
WrapperSelector (class in featureselection)
writeMappedFile() (featureselection.NetworkSelector method)
writeRankingToFile() (featureselection.FeatureSelector method)
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