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Project: systemsgenetics
(GitHub Link)
systemsgenetics-master
Genotype-IO
src
main
resources
log4j.properties
shell
index-haps.sh
java
org
molgenis
genotype
AbstractGenotypeData.java
Sequence.java
modifiable
GenotypeModificationException.java
ModifiableGenotypeDataInMemory.java
ModifiableGenotypeData.java
ModifiableGeneticVariantIterator.java
ModifiableGeneticVariant.java
SimpleSequence.java
Alleles.java
AbstractRandomAccessGenotypeData.java
GenotypedDataWriterFormats.java
bgen
TmpTest.java
BgenixMetadata.java
BgenixVariantData.java
BgenGenotypeWriter.java
BgenixReader.java
BgenixWriter.java
BgenixVariantQueryResult.java
BgenGenotypeData.java
variantFilter
VariantFilterMaf.java
VariantFilterSeqPos.java
VariantIdIncludeFilter.java
VariantFilterIterable.java
VariantFilterIsSnp.java
VariantFilterIterator.java
VariantFilterMachR2.java
VariantFilterBiAllelic.java
VariantFilterSeq.java
RandomAccessGenotypeDataVariantQc.java
VariantCombinedFilter.java
VariantFilterableGenotypeDataDecorator.java
VariantQcChecker.java
VariantFilterableGenotypeData.java
VariantFilterAmbigousSnp.java
VariantFilter.java
sampleFilter
SampleCombinedFilter.java
ConvertToSampleFilterIterable.java
SampleFilteredReadOnlyGeneticVariant.java
SampleFilterableGenotypeData.java
SampleIncludedFilter.java
SampleIdIncludeFilter.java
ConvertToSampleFilterIterator.java
SampleFilter.java
SampleFilterableGenotypeDataDecorator.java
vcf
VcfGeneticVariantMeta.java
VcfVariantLineMapper.java
VcfGenotypeData.java
VcfGenotypeRecord.java
examples
BasicUsage.java
Compare2TrityperDatasets.java
FilteringSamplesAndVariants.java
Allele.java
variant
VariantLineMapper.java
GeneticVariantMeta.java
GeneticVariantMetaMap.java
AbstractGeneticVariant.java
GenotypeRecordProb.java
GeneticVariantChrPosComparator.java
GenotypeRecordMap.java
ReadOnlyGeneticVariant.java
sampleProvider
CachedSampleVariantProvider.java
SwappingSampleVariantsProvider.java
CachedSampleVariantProviderBgen.java
SampleVariantProviderBgen.java
SampleVariantUniqueIdProvider.java
SampleVariantsProvider.java
ReadOnlyGeneticVariantBgen.java
GenotypeRecordGt.java
GenotypeRecord.java
ReadOnlyGeneticVariantTriTyper.java
GeneticVariant.java
NotASnpException.java
IllegalReferenceAlleleException.java
id
ListGeneticVariantId.java
BlankGeneticVariantId.java
SingleGeneticVariantId.java
GeneticVariantId.java
range
GeneticVariantRange.java
GeneticVariantRangeSubIterator.java
GeneticVariantRangeSubIterable.java
multipart
MultiPartVariantsIterable.java
MultiPartSequencesIterable.java
IncompatibleMultiPartGenotypeDataException.java
MultiPartGenotypeData.java
table
TableGenotypeWriter.java
util
Ld.java
MafResult.java
ProbabilitiesConvertor.java
ChromosomeComparator.java
LdCalculator.java
Utils.java
GenotypeCountCalculator.java
FixedSizeIterable.java
CalledDosageConvertor.java
GenotypeDataCompareTool.java
LdCalculatorException.java
MachR2Calculator.java
MafCalculator.java
RecordIteratorCreators.java
ChrPos.java
Cache.java
plink
PlinkFileParser.java
drivers
PedFileDriver.java
MapFileDriver.java
PedMapGenotypeWriter.java
BedBimFamGenotypeWriter.java
PedMapGenotypeData.java
datatypes
PedEntry.java
MapEntry.java
readers
FamFileReader.java
MapFileReader.java
FormatPlinkChr.java
PlinkSampleAnnotations.java
BedBimFamGenotypeData.java
VariantQuery.java
oxford
HapsGenotypeWriter.java
GenGenotypeData.java
HapsGenotypeData.java
OxfordSampleFileWriter.java
OxfordSampleFile.java
GenGenotypeWriter.java
GenotypeDataException.java
GenotypeData.java
GenotypeFileType.java
GenotypeLoader.java
VariantQueryResult.java
RandomAccessGenotypeData.java
annotation
VcfAnnotation.java
CaseControlAnnotation.java
Annotation.java
SampleAnnotation.java
SexAnnotation.java
RawLineQuery.java
editable
GenotypeDataCustomVariantProvider.java
VariantInformation.java
EditableSampleVariantsProvider.java
EditableGenotypeDosageSampleVariantsProvider.java
GenotypeDataEditableProbabilities.java
GenotypeWriter.java
GenotypeDataIndex.java
snpeff
SnpEffAnnotationTranslator.java
SnpEffEffect.java
tabix
TabixQueryResult.java
TabixIndex.java
TabixQuery.java
TabixRawLineQueryResult.java
TabixRawLineQuery.java
TabixFileNotFoundException.java
Sample.java
RawLineQueryResult.java
GenotypeInfo.java
RandomAccessGenotypeDataReaderFormats.java
trityper
TriTyperAlleleAnnotation.java
TriTyperGenotypeData.java
TriTyperGenotypeWriter.java
test
resources
ldTest.vcf.gz.tbi
test3.gen
test1.vcf
chr21.imputed.head.vcf.gz
test.vcf.gz
test2.sample
test.fam
test.map
test.sample
test.haps.tab.gz.tbi
test3.sample
test10.gen
test.vcf.gz.tbi
multiPart
all_unordered.sample
chr2_vcf.vcf
chr2.vcf.gz
chr1.vcf.gz
chr2.vcf.gz.tbi
chr2.gen
all.sample
chr1.vcf.gz.tbi
chr1.gen
chr1_vcf.vcf
test8.fam
test6.bed
test.ped
test8.bed
test3.bgen
test7.bed
test7.bim
bgenExamples
example.8bits.bgen
example.2bits.bgen
haplotypes.bgen
example.1bits.bgen
genFiles
haplotypes.edited.n3.bgen
haplotypes.edited.n3.haps
haplotypes.sample
example.sample
haplotypes.haps
haplotypes.bgen.bgi
complex.31bits.bgen
complex.bgen.bgi
org_example.16bits.bgen.bgi
complex.vcf.gz
complex.vcf.gz.tbi
complex.24bits.bgen
complex.3bits.bgen
complex.5bits.bgen
complex.15bits.bgen
complex.vcf
example.sample
haplotypes.haps
complex.sample
complex.bgen
example.16bits.bgen.bgi
chr21.imputed.head.vcf.gz.tbi
test8.bim
test.tped
test7.fam
test.haps.tab.gz
test.bim
test2.gen
test6.bim
test.haps
ldTest.vcf.gz
test.vcf
test6.fam
test.bed
TriTyper
PhenotypeInformation.txt
SNPs.txt
GenotypeMatrix.dat
SNPMappings.txt
Individuals.txt
java
org
molgenis
genotype
modifiable
ModifiableGenotypeDataInMemoryTest.java
ModifiableGeneticVariantIteratorTest.java
ModifiableGeneticVariantTest.java
RandomAccessGenotypeDataReaderFormatsTest.java
bgen
BgenGenotypeWriterTest.java
BgenixReaderTest.java
BgenGenotypeDataTest.java
BgenixReaderNGTest.java
BgenixWriterNGTest.java
variantFilter
VariantFilterableGenotypeDataDecoratorNGTest.java
sampleFilter
SampleFilterGenotypeDataNGTest.java
AlleleTest.java
vcf
VcfGenotypeRecordTest.java
VcfGenotypeDataTest2.java
VcfGenotypeDataTest.java
VcfGeneticVariantMetaTest.java
variant
SwappingSampleVariantsProviderTest.java
AbstractGeneticVariantTest.java
sampleProvider
CachedSampleVariantProviderTest.java
ReadOnlyGeneticVariantTest.java
DummySampleVariantsProvider.java
multipart
MultiPartGenotypeDataTest.java
util
AssertExtended.java
MafCalculatorTest.java
LdCalculatorTest.java
UtilsTest.java
ProbabilitiesConvertorTest.java
GenotypeCountCalculatorTest.java
GenotypeDataCompareToolTest.java
ChromosomeComparatorTest.java
plink
BedBimFamGenotypeData9SamplesTest.java
BedBimFamGenotypeData6SamplesTest.java
PedMapGenotypeDataTest.java
drivers
MapFileDriverTest.java
PedFileDriverTest.java
AbstractResourceTest.java
BedBimFamGenotypeWriterTest.java
BedBimFamGenotypeData8SamplesTest.java
BedBimFamGenotypeData7SamplesTest.java
PedMapGenotypeWriterNGTest.java
oxford
HapsGenotypeDataTest.java
GenGenotypeWriterTest.java
GenGenotypeDataTest.java
HapsGenotypeWriterTest.java
annotation
VcfAnnotationTest.java
tabix
TabixIndexTest.java
TabixQueryTest.java
AllelesTest.java
trityper
TriTyperGenotypeDataFilteredSampleAndVariant.java
TriTyperGenotypeWriterTest.java
TriTyperGenotypeDataTest.java
TriTyperGenotypeDataFilteredTest.java
ResourceTest.java
pom.xml
LICENSE
README.md
cellTypeSpecificAlleleSpecificExpression
src
main
java
nl
systemsgenetics
cellTypeSpecificAlleleSpecificExpression
ASScatterPlot.java
CTSlinearRegression.java
BinomTest.java
ReadGenoAndAsFromIndividual.java
ReadAsLinesIntoIndividualSNPdata.java
Function.java
GlobalVariables.java
BetaBinomNullLikelihood.java
CTSaltBinomialLikelihood.java
CTSbinomialTest.java
BetaBinomLikelihoodForOverdispersion.java
BetaBinomialTest.java
BinomialTest.java
CTSbetaBinomialAltLikelihoodVersion2.java
UtilityMethods.java
BamOverlapChecker.java
NonPhasedEntry.java
FindBamTranscribedRegions.java
BetaBinomOverdispInSample.java
MainEntryPoint.java
CTSnullBinomialLikelihood.java
BetaBinomAltLikelihood.java
IndividualSnpData.java
PhasedEntry.java
LikelihoodFunctions.java
CTSBetaBinomialTest.java
GenomicRegion.java
test
resources
asFolder
ERR188022snps_and_as_reads.txt
ERR188228snps_and_as_reads.txt
ERR188032snps_and_as_reads.txt
ERR188048snps_and_as_reads.txt
ERR188047snps_and_as_reads.txt
ERR188024snps_and_as_reads.txt
ERR188027snps_and_as_reads.txt
ERR188049snps_and_as_reads.txt
coupling.txt
testBam.bam
TriTyperFolder
PhenotypeInformation.txt
ImputedDosageMatrix.dat
SNPs.txt
GenotypeMatrix.dat
SNPMappings.txt
Individuals.txt
locationOfFiles.txt
testBam.bam.bai
java
nl
systemsgenetics
cellTypeSpecificAlleleSpecificExpression
ASreadsTestNGTest.java
LinearModelTestNGTest.java
LikelihoodFunctionsNGTest.java
CheckMinimumhetReadsNGTest.java
pom.xml
LICENSE
README.md
javaPoCA
src
main
java
nl
umcg
bondermj
pcoa
DoPcoa.java
PcoaParamaters.java
pom.xml
BinaryMetaAnalyzer
src
main
resources
settings.xml
java
nl
umcg
bondermj
microbialmetanalysis
BinaryMicrobePcaAnalysis.java
westrah
binarymetaanalyzer
QTL.java
BinaryMetaAnalysisTask.java
InternalMetaAnalysisDataset.java
MetaQTL4TraitAnnotation.java
BinaryMetaAnalysisSettings.java
InternalMetaAnalysisTask.java
BinaryMetaAnalysisCLI.java
MetaQTL4MetaTrait.java
MatrixConverter.java
MetaQTL4MetaTraitTreeSet.java
BinaryMetaAnalysisDataset.java
MatrixConverterCis.java
InternalMetaAnalysisSettings.java
westrah
binarymetaanalyzer
posthoc
CompareQTLEffectSizes.java
ProbeRename.java
ld
SortedBinaryZScoreFile.java
BinaryLDMatrixConverter.java
BinaryFileLD.java
BinaryFileSorter.java
SortedBinaryZDataBlock.java
CheckZScoreMeanAndVariance.java
ApplyFDR.java
CompareSNPProbeCombosBetweenFiles.java
BHFDR.java
SplitQTLFile.java
QTLReplicationTable.java
IndependentDatasetAnalyzer.java
QTLFileFilter.java
FDRFilter.java
EQTLFileR2Calculator.java
SettingsFileCreator.java
NullSetGenerator.java
InternalMetaAnalysis.java
BinaryMetaAnalysis.java
pom.xml
pom.xml
DEPICT2
src
main
resources
verion.properties
bash
ConvertSummaryStatistics.sh
SubmitDepict2RunCalculon.sh
CalculateAUC.sh
EchoDepict2Command.sh
SubmitDepict2Run.sh
Depict2Run.sh
java
ch
unil
genescore
vegas
DaviesBigDecimal.java
Davies.java
FarebrotherBigDecimal_1.java
FarebrotherBigDecimal.java
WeightedChisquareAlgorithm.java
Farebrother.java
nl
systemsgenetics
depict2
runners
NetworkProperties.java
TestCoregulationPerformance.java
ConvertGtexGct.java
Depict2.java
development
sophie
TraitFileClean.java
GenerateRandomNullData.java
GenerateRandomNullDataOther.java
TraitFile.java
ExploreCoregulationMatrix.java
Test.java
originalLude
PerformDEPICT2Analysis.java
EstimateChi2SumDistUsingCorrelatedVariablesThread.java
ExpressionDataset.java
DoubleArrayIntegerObject.java
TestBigDecimal.java
BinaryCompareFormat.java
First1000qtl.java
ExtractCol.java
InfoOnlyLogLayout.java
Depict2Mode.java
Depict2Options.java
PcaData.java
gene
CalculateGeneInvCorMatrix.java
JamaHelperFunctions.java
GenePvalueCalculator.java
GenotypeCorrelationSource.java
GeneWeightCalculator.java
GenotypeCorrelationGenotypes.java
Gene.java
io
IoUtils.java
GwasSummStats.java
ExcelWriter.java
pathway
PathwayAnnotations.java
PathwayDatabase.java
PathwayEnrichmentsOld.java
PathwayEnrichments.java
ChrPos.java
r
depict2
depict2_post_procces.r
depict2_make_coregulation_nodes_and_edges.r
examples
kidney
kidneyExample.R
kidney_network_edges.r
coeliac
depict2_CeD_plots.rmd
height
height_auc_comparison.R
heightAucTest.R
height_comparing_genep_coreg_correlations.r
depict2_network_plot.r
.RData
depict2.Rproj
depict2_network_plot_backup_9-12-2019.r
testing_scripts
ddAucTest.R
testCalculateGeneScores.R
comparision_plots.r
gene_gene_correlations.R
depict2_CeD_comparison.r
GLS_experiments_2.R
GLS_experiments.R
depict2_glm_comparision.rmd
marfanFibroblast.R
gwasRareDiseaseEnrichment.R
assembly
assembly.xml
test
resources
gwasGeneScores.txt
pathwayGeneScores.txt
testMatrix.R
invCor1p.txt
runDemo.sh
gwasGeneScoresNull.txt
invCorMatrix.txt
demoFiles
demoGenes.txt
demoGenotypes.vcf.gz.tbi
demoGwas.rows.txt
demoGwas.cols.txt
demoGenotypes.vcf.gz
demoGwas.dat
demoSamples.txt
identity1q.txt
invCor1q.txt
idenity4x4.txt
identity1p.txt
java
nl
systemsgenetics
depict2
PathwayEnrichmentsTest.java
pom.xml
Decon2
example_data
fake_genotypes.py
predicted.cellcounts.scaled.txt
gene_snp_file.txt
LICENSE
GraphicalAbstractDecon2_v3.jpg
DeconCell
NAMESPACE
inst
doc
my-vignette.R
my-vignette.Rmd
vignettes
my-vignette.Rmd
DESCRIPTION
DeconCell.Rproj
.Rbuildignore
data
dCell.names.RData
cell.proportions.RData
dCell.geneList.RData
README.md
man
glmnet.wrapper.Rd
dCell.run.Rd
dCell.predict.Rd
dCell.predict.single.Rd
dCell.run.single.Rd
dCell.models.Rd
dCell.names.Rd
dCell.geneList.Rd
count.table.Rd
dCell.expProcessing.Rd
cell.proportions.Rd
dCell.exp.trimming.Rd
dCell.evaluate.Rd
get.marker.genes.Rd
R
dCell_functions.R
data.R
.gitignore
README.md
Decon-eQTL
src
main
resources
project.properties
java
decon_eQTL
DeconvolutionResult.java
DeconvolutionLogger.java
CellCount.java
Utils.java
InteractionModel.java
NumericRuntimeException.java
NonNegativeLeastSquares.java
Main.java
CommandLineOptions.java
Deconvolution.java
GenotypeData.java
TooManyIterationsException.java
ExpressionData.java
Statistics.java
CustomRecordFormatter.java
InteractionModelCollection.java
test
resources
simulated_expression
simulation_code
simulate_celltypeSpecific_eQTL.py
simulate_celltypeSpecific_effect_eQTL_diffSamples.py
genotype_files
genotype_dosages.txt
expression_files
expression_levels_wrong_names.txt
expression_levels.txt
cellcount_files
cellcounts.txt
cellcounts_small.txt
expected_results
deconSpearmanExpected.txt
deconExpected.txt
deconRoundDosageExpected.txt
expectedPredictedExpressionLevels.txt
gene_snp_list_files
gene_snp_list_non_existing_genotype.txt
gene_snp_list_long.txt
gene_snp_list.txt
gene_snp_list_non_existing_gene.txt
java
decon_eQTL
StatisticsTest.java
UtilsTest.java
DeconvolutionTest.java
pom.xml
README.md
.gitignore
doc
package-list
script.js
overview-summary.html
Decon_eQTL
package-frame.html
Utils.html
InteractionModelCollection.html
CommandLineOptions.html
ExpressionData.html
TooManyIterationsException.html
class-use
Utils.html
InteractionModelCollection.html
CommandLineOptions.html
ExpressionData.html
TooManyIterationsException.html
Qtl.html
NotEnoughSamplesPerGenotypeException.html
GenotypeData.html
Statistics.html
CellCount.html
NumericRuntimeException.html
DeconvolutionLogger.html
InteractionModel.html
DeconvolutionResult.html
PermutationTest.html
NonNegativeLeastSquares.html
Deconvolution.html
NotEnoughGenotypesException.html
package-tree.html
Qtl.html
NotEnoughSamplesPerGenotypeException.html
GenotypeData.html
Statistics.html
CellCount.html
NumericRuntimeException.html
DeconvolutionLogger.html
InteractionModel.html
DeconvolutionResult.html
PermutationTest.html
package-summary.html
NonNegativeLeastSquares.html
Deconvolution.html
package-use.html
NotEnoughGenotypesException.html
overview-frame.html
overview-tree.html
serialized-form.html
help-doc.html
constant-values.html
deprecated-list.html
index-files
index-14.html
index-16.html
index-7.html
index-17.html
index-10.html
index-2.html
index-3.html
index-12.html
index-9.html
index-5.html
index-11.html
index-6.html
index-13.html
index-1.html
index-8.html
index-4.html
index-15.html
allclasses-frame.html
deconvolutionTests
package-frame.html
class-use
DeconvolutionTest.html
package-tree.html
DeconvolutionTest.html
package-summary.html
package-use.html
allclasses-noframe.html
index.html
stylesheet.css
.gitignore
LICENSE
lib
MetaGenomicDataProcessing
src
main
java
umcg
genetics
tableAdaption
NormalizeToReadsPerMillion.java
PrintTablePerLevel.java
ExtendSnpProbeCombinationsFile.java
NormalizeAndFilter.java
PrintPerDatasetCuttOff.java
PrintDatasetPerEntry.java
test
java
org
MetaGenomicDataProcessing
AppTest.java
pom.xml
Genotype-Harmonizer
src
main
resources
verion.properties
java
nl
umcg
deelenp
genotypeharmonizer
GenotypeAlignmentException.java
GenotypeHarmonizer.java
GenotypeHarmonizerParamaters.java
SnpLogWriter.java
Aligner.java
scripts
HarmonizeShapeit2HapsExample.bat
HarmonizeShapeit2HapsExample.sh
GenotypeHarmonizer.sh
HarmonizeBinaryPlinkExample.sh
GenotypeHarmonizer.bat
HarmonizeBinaryPlinkExample.bat
assembly
assembly.xml
test
resources
hapmap3CeuChr20B37Mb6RandomStrand.bim
hapmap3CeuChr20B37Mb6.fam
hapmap3CeuChr20B37Mb6RandomStrand.fam
hapmap3CeuChr20B37Mb6RandomStrand.bed
hapmap3CeuChr20B37Mb6RandomStrand.log
hapmap3CeuChr20B37Mb6.bim
1000gCeuChr20Mb6.vcf.gz.tbi
sampleFilterTestList.txt
IncludedByKeep.txt
hapmap3CeuChr20B37Mb6RandomStrand.sample
hapmap3CeuChr20B37Mb6.bed
java
nl
umcg
deelenp
genotypeharmonizer
GenotypeHarmonizerTest.java
nb-configuration.xml
nbactions-testVcf.xml
pom.xml
LICENSE
nbactions-testldHapmap.xml
README.md
eqtl-functional-enrichment
src
main
java
nl
systemsgenetics
eqtlpermutationtranscriptionfactoranalysis
GwasEnrichment.java
eQtlsInEncodeAnnotationDataRegions.java
eQtlAndLdInRepeatRegions.java
SameNarrowPeakRegions.java
EQtlPermutationTranscriptionFactorAnalysisV3.java
EQtlPermutationTranscriptionFactorAnalysisV2.java
eQtlDataParser.java
EQtl.java
HistoneSiteEnrichment.java
eQtlAndLdInRepeatRegions2.java
EQtlPermutationTranscriptionFactorAnalysis.java
Testing.java
eQtlsInRepeatData.java
eQtlsInEncodeAnnotationData.java
RepeatElement.java
eQtlsInEncodePseudogenes.java
CombineNarrowPeakFiles.java
WriteWigToText.java
SplitWigTextDataOnChromosome.java
eQtlsInAluRipData.java
EnrichmentDataReader.java
TranscriptionFactorEnrichmentV2.java
eQtlsInPseudogeneOrgData.java
NarrowPeakElement.java
eqtlannotation
EncodeNarrowPeak.java
TfbsOverlapResult.java
RoadMapCHmm.java
SNP.java
Bed.java
ChmmState.java
EncodeMultipleTfbsOverlap.java
EncodeTfbsOverlap.java
summarizeTfbsOutput.java
pom.xml
GeneNetworkBackend
src
main
java
nl
systemsgenetics
genenetworkbackend
hpo
EffectOfRandom10Percent.java
IdentifyOutlierHhoAssignments.java
InvestigateAucChildParent.java
HpoGenePrioritisation.java
processCaseHpo.java
Test.java
PlayingWithHpoOntology.java
FilterPrioBasedOnMutatedGenes2.java
FilterPrioBasedOnMutatedGenes.java
TestDiseaseGenePerformance.java
DiseaseGeneHpoData.java
ImproveHpoPredictionBasedOnChildTerms.java
PredictionInfo.java
HpoOntology.java
SkewnessInfo.java
GenePrioritisationResult.java
HpoFinder.java
ConvertHpoToMatrixWith10ProcentRandom.java
ConvertMyoclonusClustersToMatrix.java
ConvertHpoToMatrix.java
div
MergeGavinPrioritization.java
ParseLog.java
InvestigateBav.java
Test.java
CreateCgdMatrix.java
InvestigateMyoclonus.java
ExtactGenesPerCase.java
ExctractAnnotatedGenes.java
InvestigateString.java
CompareGenePredictability.java
ConvertTfDataUrmoToMatrix.java
CountCorAboveThreshold.java
CalculateGenePredictability.java
ConvertGmtToMatrix.java
SpikeInKnownAnnotations.java
PredictGenesetMembers.java
ConvertReactomeToMatrix.java
predictions
ExpressionDatasetInt.java
ExpressionDataset.java
ExpressionDatasetBool.java
PredictGenesetMemberBasedOnTCs.java
WilcoxonMannWhitney.java
ConvertGoToMatrix.java
RecalculateAuc.java
PredictGenesetMembersOptions.java
pom.xml
README.md
README.md
GadoCommandline
src
main
resources
verion.properties
java
nl
systemsgenetics
gadocommandline
HpoGenePrioritisation.java
InfoOnlyLogLayout.java
GadoMode.java
GadoCommandline.java
PredictionInfo.java
HpoOntology.java
GadoOptions.java
ProcessCaseHpo.java
GenePrioritisationResult.java
HpoFinder.java
assembly
assembly.xml
pom.xml
imputation-tool
src
main
java
imputationtool
postprocessing
CompareImputedSNPsToRealSNPs.java
TriTyperDatasetCorrelator.java
TriTypertoPedMapDatExcludedSNPAnalyzer.java
BeagleImputationQuality.java
ScatterPlot.java
ImputationSNPPresenceCheck.java
ImputationTool.java
preprocessing
BatchGenerator.java
DetermineLD.java
pom.xml
README.md
genetica-libraries
src
main
resources
regulomeDbTestFile2.txt
regulomeDbTestFileEmpty.txt
regulomeDbTestFile.txt
java
umcg
genetica
gwas
Independifier.java
Dependifier.java
containers
StringDoubleObject.java
Chromosome.java
StringIntegerObject.java
Triple.java
SortableSNP.java
Transcript.java
Pair.java
Exon.java
Gene.java
enums
Gender.java
DiseaseStatus.java
Strand.java
SNPClass.java
Chromosome.java
ChromosomeUCSC.java
graphics
ViolinBoxPlot.java
ForestPlot.java
Grid.java
themes
ComplementaryColor.java
ColorBlindTheme.java
DefaultTheme.java
Theme.java
ChromosomePlot.java
DefaultGraphics.java
VennDiagram.java
panels
SpacerPanel.java
DensityGraphPanel.java
ScatterplotPanel.java
BoxPlotPanel.java
AnnotationTrackPanel.java
HistogramPanel.java
AnnotationPanel.java
CircularHeatmapPanel.java
LDPanel.java
GraphAnnotationPanel.java
HeatmapPanel.java
RSquaredPanel.java
Panel.java
GenePanel.java
LegendPanel.java
AssociationPanel.java
DonutGraphPanel.java
Heatmap.java
ColorGenerator.java
Range.java
ScatterPlot.java
methylation
ConvertBetaAndMvalues.java
AssociatingPcasWithAnnotation.java
DeepCopy.java
ParseTcgaMethylationFile.java
CheckMatrixForValidBetaValues.java
MethylationAssociatoingAnnotationWithValues.java
SoftfileAnnotation.java
ConverteUandMTo.java
util
WriteFastaOfInterestRegion.java
RankArray.java
InplaceArrayQuickSort.java
RunTimer.java
WriteExtendedFastaOfInterestRegion.java
CheckAssocationMultipleGeneProbes.java
VectorSorter.java
StringIntegerObjectSorterSortOnInteger.java
Primitives.java
StringDoubleObjectSorterSortOnDouble.java
RankIntArray.java
MultiThreadedInPlaceQuickSort.java
RankDoubleArray.java
ConverteMappingAndSnpFile.java
SmoothSort.java
individuals
Family.java
Individual.java
console
MultiThreadProgressBar.java
ProgressBar.java
ConsoleGUIElems.java
ensembl
Features.java
io
pileup
PileupToVcf.java
PileupFile.java
PileupParseException.java
PileupEntry.java
regulomedb
RegulomeDbIterator.java
RegulomeDbSupportingData.java
RegulomeDbEntry.java
RegulomeDbFiles.java
RegulomeDbFile.java
gwascatalog
GWASCatalog.java
GWASTrait.java
GWASLocus.java
GWASPublication.java
GWASSNP.java
gmt
GMTFile.java
plink
PedAndMapFunctions.java
SampleAnnotation.java
PlinkFamFile.java
binInteraction
variant
BinaryInteractionVariantAbstract.java
BinaryInteractionVariantCreator.java
BinaryInteractionVariant.java
BinaryInteractionVariantStatic.java
BinaryInteractionFileException.java
BinaryInteractionFileConstructorBuilder.java
BinaryInteractionQtlZscores.java
BinaryInteractionQueryResult.java
BinaryInteractionFile.java
gene
BinaryInteractionGeneStatic.java
BinaryInteractionGeneAbstract.java
BinaryInteractionGene.java
BinaryInteractionGeneCreator.java
BinaryInteractionCohort.java
BinaryInteractionCovariateIterator.java
BinaryInteractionFileCreator.java
BinaryInteractionZscores.java
ucsc
PeakFile.java
UCSCDataObject.java
WigFile.java
UCSCTrack.java
chrContacts
SortIntraChrContacts.java
DesiredChrContact.java
SortInterChrContacts.java
ChrContact.java
concurrent
DoubleParseTask.java
text
TextFile.java
converters
NetworkConverter.java
bin
RandomAccessFile.java
BinaryFile.java
bed
BedEntry.java
BedFile.java
fasta
ReferenceGenomeFasta.java
LargeByteArray.java
gtf
GffReaderInterface.java
GffAttributeFilter.java
TestGffIntervalTree.java
GffElement.java
GffElementIterator.java
GtfReader.java
geofiles
ParseTextTable.java
ParseSoftFile.java
probemapping
reading.java
trityper
EQTL.java
WGAFileMatrixGenotype.java
QTLTextFile.java
WGAFileMatrixRawData.java
TriTyperSNPMappings.java
ConvertHLAHaplotypesToTriTyper.java
SNPLoader.java
WGAFileMatrixImputedDosage.java
SNP.java
probeannotation
ProbeTranslation.java
ProbeAnnotation.java
ProbeAnnotation.java
BufferedSNPLoader.java
util
ChrAnnotation.java
TriTyperGenotypeDataMerger.java
BaseAnnot.java
CompareAllelicDirections.java
TriTyperConcatDatasets.java
DetermineLD.java
converters
TriTyperToVCF.java
TriTyperToMachImputedTransposed.java
InversionCallsToTriTyper.java
PedAndMapToTriTyper.java
MachImputedTransposedDosageToTriTyper.java
TriTyperToTabSeparated.java
BeagleImputedToTriTyper.java
TriTyperToPlinkDosage.java
TriTyperReferenceConcordantPedAndMapExporter.java
MinimacImputedToTriTyper.java
PlinkDosageToTriTyper.java
VCFToTriTyper.java
FinalReportToTriTyper.java
MachImputedToTriTyper.java
TriTyperToPedAndMapConverter.java
TriTyperToDosageConverter.java
ImputeImputedToTriTyperV2.java
TriTyperGeneticalGenomicsDataset.java
TriTyperGenotypeData.java
ConvertDoubleMatrixDataToTriTyper.java
MinimalEQTL.java
TriTyperGeneticalGenomicsDatasetSettings.java
bin
BinaryResultDataset.java
BinaryResultSNPSummary.java
BinaryResultProbeSummary.java
BinaryResultProbe.java
BinaryResultSNP.java
BinaryGZipFloatMatrix.java
TriTyperExpressionData.java
Gpio.java
bedgraph
BedGraphFile.java
BedGraphEntry.java
collections
ChrPosTreeMap.java
intervaltree
PerChrIntervalTree.java
RangeEndReverseComparator.java
RangeStartComparator.java
IntervalTree.java
StringRange.java
IntervalTreeNode.java
Range.java
NamedGenomicRange.java
ChrPosMap.java
math
PCA.java
interpolation
CubicSpline.java
PCAojAlgo.java
PcaColt.java
matrix2
DoubleMatrixDatasetRandomAccessTranspose.java
DoubleMatrixDataset.java
DoubleMatrixDatasetAppendableWriter.java
DoubleMatrix1dOrder.java
MatrixHandling.java
DoubleMatrixDatasetRandomAccessReader.java
DoubleMatrixDatasetRowIterable.java
DoubleMatrixConverter.java
MatrixTools.java
DoubleMatrixDatasetFastSubsetLoader.java
MergeDoubleMatrices.java
DoubleMatrixDatasetRandomAccessWriter.java
stats
QuantileNormalizationToReference.java
WeightedCorrelations.java
FisherExactTest.java
Heterogeneity.java
Correlation.java
Log2Transform.java
AndersonDarling.java
PearsonRToZscoreBinned.java
QValues.java
Binning.java
Regression.java
VIF.java
Normalization.java
TheilSen.java
HWE.java
QuantileNormalization.java
ChiSquare.java
concurrent
ConcurrentBrayCurtis.java
ConcurrentCovariation.java
ConcurrentCorrelation.java
ConcurrentCityBlockTask.java
ConcurrentCovariationTask.java
ConcurrentBrayCurtisTask.java
ConcurrentCorrelationTask.java
ConcurrentCityBlock.java
TTest.java
ZScores.java
FDRUtils.java
MannWhitneyUTest2.java
KolmogorovSmirnov.java
TwoStepLeastSquares.java
Descriptives.java
WilcoxonMannWhitney.java
AUC.java
matrix
DoubleMatrixDataset.java
DoubleMatrixDatasetAC.java
SymmetricShortDistanceMatrix.java
SymmetricByteDistanceMatrix.java
MatrixHandling.java
SymmetricFloatDistanceMatrix.java
MatrixTools.java
MergeDoubleMatrices.java
DoubleMatrixDatasetRA.java
Fmath.java
Goniometry.java
features
NarrowPeakFeature.java
Probe.java
SNPFeature.java
GFFFile.java
FeatureType.java
PeakFeature.java
Track.java
FeatureMerger.java
BedFileGroup.java
BedFileFeature.java
Transcript.java
Feature.java
BedGraphFeature.java
Exon.java
FeatureTree.java
Gene.java
UTR.java
FeatureComparator.java
variantAnnotator
GenomicRange.java
VariantAnnotator.java
legacy
ParseSOFTFile.java
ExpressionDataset.java
text
parsing
Demographics.java
Strings.java
genomicboundaries
GenomicBoundariesIterator.java
GenomicBoundariesSimple.java
GenomicBoundaries.java
GenomicBoundary.java
ncbi
dbsnp
SNPAnnotation.java
com
mastfrog
util
streams
HashingOutputStream.java
HashingInputStream.java
test
resources
testMatrixColumnWeightedCorMatrix.txt
generateTestMatrix.R
testMatrix.txt
wgEncodeCrgMapabilityAlign50mer.bedGraph
testMatrixColumnCorZscoreMatrix.txt
randomWeights.txt
testMatrixColumnCovMatrix.txt
testMatrixColumnScaledMatrix.txt
createTestMatrixDerivatives.R
testMatrixColumnCorMatrix.txt
createReferencePcaFiles.R
java
umcg
genetica
util
inplaceArrayQuickSortNGTest.java
SmoothSortTest.java
MultiThreadedInPlaceQuickSortNGTest.java
RankArrayNGTest.java
io
pileup
PileupEntryTest.java
regulomedb
RegulomeDbFileNGTest.java
RegulomeDbSupportingDataNGTest.java
RegulomeDbEntryNGTest.java
RegulomeDbFilesNGTest.java
binInteraction
BinaryInteractionFileTest.java
fasta
LargeByteArrayTest.java
bedgraph
BedGraphFileTest.java
collections
ChrPosMapTest.java
intervaltree
IntervalTreeTest.java
math
matrix2
DoubleMatrixDatasetTest.java
DoubleMatrixDatasetRowIterableTest.java
PcaColtNGTest.java
stats
CorrelationNGTest.java
DescriptivesNGTest.java
CorrelationTest.java
MannWhitneyUTest2NGTest.java
PearsonRToZscoreBinnedNGTest.java
WeightedCorrelationsTest.java
ZScoresTest.java
QuantileNormalizationNGTest.java
genomicboundaries
GenomicBoundaryTest.java
GenomicBoundariesTest.java
nb-configuration.xml
pom.xml
testInt3.bin
testInt2.bin
testInt1.bin
nbactions-gffTest.xml
.gitignore
eQTLInteractionAnalyser
src
main
java
nl
systemsgenetics
eqtlinteractionanalyser
eqtlinteractionanalyser
CompareToGeuvadis.java
DoubleArrayIntegerObjectSorter.java
EQTLInteractionAnalyser.java
GeneAnnotation.java
InteractionPlotter.java
VectorSorter.java
ExpressionDataset.java
StringIntegerObject.java
createOptionsListForManual.java
StringIntegerObjectSorter.java
SkippedInteractionWriter.java
SkippedInteractionTracker.java
TestEQTLDatasetForInteractions.java
PerformInteractionAnalysisPermutationTask.java
DoubleArrayIntegerObject.java
test
java
nl
systemsgenetics
eqtlinteractionanalyser
AppTest.java
pom.xml
FunctionEnrichmentOfTransQtls
src
main
java
nl
systemsgenetics
functionenrichmentoftransqtls
FunctionEnrichMain.java
ConvertToChiSq.java
CorrelateSumChi2ToPathways.java
pom.xml
GeneticRiskScoreCalculator
src
main
java
nl
systemsgenetics
simplegeneticriskscorecalculator
RiskEntry.java
CalculateSimpleGeneticRiskScore.java
Main.java
benchmark
Benchmark.java
geneticriskscorecalculator
GeneticRiskScoreCalculator.java
PhenotypeData.java
Configuration.java
Main.java
SimpleGeneticRiskScoreCalculator.java
RiskScoreMatrix.java
GwasCatalogLoader.java
assembly
assembly.xml
pom.xml
LICENSE
README.md
eqtl-mapping-pipeline
src
main
resources
settings.xml
transSnps.txt.gz
version.properties
java
eqtlmappingpipeline
binaryInteraction
ConvertTextOutputToBinary.java
ReplicateInteractions.java
InvestigateCovariate.java
QueryBinaryInteraction.java
BinaryInteractionMetaAnalysis.java
CovariateImportance.java
trans
TransQTL.java
TransQTLEncoder.java
metaqtl4
MetaQTL4ExecutionTask.java
MetaQTL4TraitAnnotation.java
MetaQTL4CorrelationTask2.java
MetaQTL4BinaryResultFile.java
MetaQTL4CorrelationTask.java
MetaQTL4Dataset.java
SingleDatasetAnalysisTask.java
MetaQTL4.java
MetaQTL4QTL.java
SingleDatasetAnalysis.java
MetaQTL4MetaTrait.java
MetaQTL4DatasetSettings.java
MetaQTL4MetaTraitTreeSet.java
MetaQTL4Settings.java
MetaQTL4ConsoleUI.java
mixupmapper
MixupMapperVisualization.java
MixupMapperConsoleGUI.java
containers
Trio.java
Matrix.java
Family.java
Individual.java
MixupMapper.java
stat
PCA.java
dist
Bin.java
Dist.java
DiscreteDist.java
transCorrelationQtl
MetaTRansCorrelationQtlResult.java
PvalueZscore.java
MetaTransCorrelationQtl.java
ExtractDataForPlots.java
RtoPandZ.java
transCorrelationQtl.java
Qtl.java
qcpca
QCPCAConsoleGui.java
QCPCA.java
graphics
histogram
FrequencyDistributionHistogram.java
MultiFrequencyDistributionHistogram.java
Histogram.java
MultiDistrubutionHistogram.java
map
MixupMapperHeatMap.java
Heatmap.java
Graphics.java
ScatterPlot.java
curve
Curve.java
ROCCurve.java
util
QTLLookup.java
ReplaceQTL.java
ExpressionSampleFilter.java
NoLdSnpProbeListCreator.java
ConvertTOSMRFormat.java
HiC
HiCQTLProbeAnnotatorSnpBased.java
HiCQTLAnnotatorSnpBased.java
HiCQTLAnnotatorBlockbased.java
GetStatistics.java
ProbeSNPMapper.java
ReplaceBeta.java
QTLFileSorter.java
TriTyperSplitter.java
ExpressionFileMerger.java
ExpressionDataQuery.java
QTLFileMerger.java
UtilConsoleGUI.java
QTLFileCompare.java
ProbeSpecificFDR.java
SummarizeQtlSummaries.java
ModuleEqtlGeuvadisReplication.java
LDCalculator.java
BinaryResultFileConverter.java
RegressCisEffectsFromGeneExpressionData.java
GetMAFFromSNPQCLog.java
ModuleEqtlNeutrophilReplication.java
BatchSplitter.java
QTLDotPlotter.java
QTLAnnotator.java
ModuleEqtWestraReplication.java
GenotypeDataMerger.java
CisEQTLProbeSNPLDCheck.java
BinaryMatrixConverter.java
QTLFileSplitter.java
GenotypeDataQuery.java
interactionanalysis
InteractionPlotter.java
InteractionAnalysisResults.java
InteractionAnalysisTask.java
InteractionAnalysisMultiThreaded.java
InteractionAnalysisConsoleGUI.java
InteractionAnalysisDetermineDirection.java
gui
EQTLMappingPipelineConsole.java
Main.java
binarymeta
util
Filter.java
SNPAlleleCheck.java
Main.java
meta
MetaAnalysisPlotThread.java
Reader.java
MetaAnalysisResultThread.java
IndividualAnalysis.java
graphics
PlotPackage.java
ZScorePlotThread.java
ZScorePlot.java
MultiVenn.java
PValueThreshold.java
Result.java
MetaSettings.java
cis
UnzipTask.java
ZScoreLoaderTask.java
CisBinaryConverter.java
ResultProcessor.java
CalcThread.java
CisAnalysis.java
BinaryUnzipTask.java
MetaAnalysisLoaderThread.java
MetaAnalysisWorkPackage.java
MetaAnalyze.java
ZScoreComparison.java
MetaAnalysisCalculationThread.java
conditionalanalysis
ConditionalAnalysisConsoleGUI.java
ConditionalAnalysis.java
IterativeConditionalAnalysis.java
pcaoptimum
PCAOptimumPlot.java
PCAOptimumConsoleGUI.java
PCAOptimumInventorize.java
PCAOptimum.java
eQTLFoldChangeCalculator
QTLFoldChangeCalculator.java
QTLFoldChangeCalculatorGUI.java
textmeta
FixedEffectMetaAnalysis.java
FixedEffectMetaAnalysisTask.java
ase
AseResults.java
MultipleTestingCorrectionMethod.java
AseVariantBean.java
AseException.java
AnnotateAseWithSnpEffVcf.java
AseMleNegative.java
AseRecalculate.java
FindMatchingSnps.java
AseMleBeta.java
CompareAseToEqtl.java
AseMle.java
SnpEffAnnotationMap.java
NewMain.java
AseConfiguration.java
CompareAseFiles.java
Ase.java
AseVariant.java
AseVariantRecalculate.java
AseVariantAppendable.java
ReadCountsLoader.java
AseCalculator.java
chromosomeyexpressionplotter
ChromosomeYExpressionPlotter.java
ChromosomeYExpressionPlot.java
ChrYExpressionPlotConsoleGUI.java
metaqtl3
ReadPermutationFile.java
containers
QTL.java
WorkPackage.java
Result.java
QTLResultContainer.java
TextResult.java
Settings.java
MetaQTL3.java
graphics
QQPlot.java
EQTLDotPlot.java
EQTLPlotter.java
FDR.java
WorkPackageProducer.java
EQTLRegression.java
CalculationThread.java
MetaQTL3ConsoleGUI.java
ResultProcessorThread.java
causalinference
IVAnalysis.java
Mediation.java
IVConsoleGUI.java
normalization
Normalizer.java
NormalizationConsoleGUI.java
org
apache
commons
math3
stat
inference
AlternativeHypothesis.java
BinomialTest.java
scripts
create.tstat.matrix.R
test.mappings.R
helper.functions.R
rnaseq.analysis.R
create.tstat.matrix.illumina.R
tstat.postprocessing.R
assembly
assembly.xml
test
resources
GeuvadisTestData
snpProbeCombinations_transQTL.txt
settings.xml
TestOutput
Cis-CEU-eQTLsFDR0.05.txt
Trans-Meta-eQTLsFDR0.05-ProbeLevel.txt
Geuvadis_CEU_gte.txt
Geuvadis_CEU_YRI_Annot.txt
Geuvadis_chr2.vcf.gz.tbi
Geuvadis_chr1.vcf.gz.tbi
Geuvadis_YRI_gte.txt
trityper
PhenotypeInformation.txt
SNPs.txt
SNPMappings.txt
Individuals.txt
java
eqtlmappingpipeline
binaryInteraction
BinaryInteractionMetaAnalysisTest.java
CreateGeuvadisTestTrityper.java
FullQtlMappingCisTest.java
FullQtlMappingTransMetaTest.java
SmoothSortQtlTest.java
ase
AseMleBetaTest.java
AseMleTest.java
AseVariantTest.java
NormalizationTest.java
metaqtl3
CalculationThreadTest.java
nb-configuration.xml
pom.xml
LICENSE
README_old.md
README.md
nbactions-testAse.xml
Systems Genetics
See:
http://www.molgenis.org/systemsgenetics/
Or see the readme files of the different modules