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Files of the artifact somatic version 1.4.0 from the group org.campagnelab.dl.

Artifact somatic
Group org.campagnelab.dl
Version 1.4.0
Last update 15. November 2017
Tags: networks project mutations recognize data train neural
Organization not specified
URL Not specified
License not specified
Dependencies amount 11
Dependencies fastutil, deeplearning4j-core, deeplearning4j-nlp, guava, commons-io, logback-classic, logback-core, protobuf-java, dsiutils, jcommander, commons-math3,
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Source code of somatic version 1.4.0

META-INF

META-INF.META-INF.MANIFEST.MF

META-INF.maven.org.campagnelab.dl.somatic

META-INF.maven.org.campagnelab.dl.somatic.META-INF.maven.org.campagnelab.dl.somatic.pom.properties

META-INF.maven.org.campagnelab.dl.somatic.META-INF.maven.org.campagnelab.dl.somatic.pom.xml

META-INF.services

META-INF.services.META-INF.services.org.campagnelab.goby.predictions.SomaticPredictor

.VARIATION_COMMIT.properties

org.campagnelab.dl.somatic.genotypes

org.campagnelab.dl.somatic.genotypes.org.campagnelab.dl.somatic.genotypes.BaseGenotypeCountFactory

org.campagnelab.dl.somatic.genotypes.org.campagnelab.dl.somatic.genotypes.GenotypeCountFactory

org.campagnelab.dl.somatic.intermediaries

org.campagnelab.dl.somatic.intermediaries.org.campagnelab.dl.somatic.intermediaries.FilteredNonFiltered

org.campagnelab.dl.somatic.intermediaries.org.campagnelab.dl.somatic.intermediaries.FirstSimulationStrategy

org.campagnelab.dl.somatic.intermediaries.org.campagnelab.dl.somatic.intermediaries.Intermediary

org.campagnelab.dl.somatic.intermediaries.org.campagnelab.dl.somatic.intermediaries.OneSampleCanonicalSimulationStrategy

org.campagnelab.dl.somatic.intermediaries.org.campagnelab.dl.somatic.intermediaries.QuickConcatArguments

org.campagnelab.dl.somatic.intermediaries.org.campagnelab.dl.somatic.intermediaries.Randomizer

org.campagnelab.dl.somatic.intermediaries.org.campagnelab.dl.somatic.intermediaries.SimulationCharacteristics

org.campagnelab.dl.somatic.intermediaries.org.campagnelab.dl.somatic.intermediaries.SimulationStrategy

org.campagnelab.dl.somatic.intermediaries.org.campagnelab.dl.somatic.intermediaries.ThreeSampleSimulationStrategyImplTrio

org.campagnelab.dl.somatic.intermediaries.org.campagnelab.dl.somatic.intermediaries.TwoSampleCanonicalSimulationStrategy

org.campagnelab.dl.somatic.intermediaries.org.campagnelab.dl.somatic.intermediaries.TwoSampleSimulationStrategyTrio

org.campagnelab.dl.somatic.learning

org.campagnelab.dl.somatic.learning.org.campagnelab.dl.somatic.learning.AUCLossCalculator

org.campagnelab.dl.somatic.learning.org.campagnelab.dl.somatic.learning.AbstractPredictMutations

org.campagnelab.dl.somatic.learning.org.campagnelab.dl.somatic.learning.PredictMutations

org.campagnelab.dl.somatic.learning.org.campagnelab.dl.somatic.learning.PredictionArguments

org.campagnelab.dl.somatic.learning.org.campagnelab.dl.somatic.learning.SomaticTrainer

org.campagnelab.dl.somatic.learning.org.campagnelab.dl.somatic.learning.SomaticTrainingArguments

org.campagnelab.dl.somatic.learning.org.campagnelab.dl.somatic.learning.TrainModelS

org.campagnelab.dl.somatic.learning.org.campagnelab.dl.somatic.learning.TrainSomaticModel

org.campagnelab.dl.somatic.learning.org.campagnelab.dl.somatic.learning.TrainSomaticModelErrorSampling

org.campagnelab.dl.somatic.learning.org.campagnelab.dl.somatic.learning.TrainSomaticModelOnGPU

org.campagnelab.dl.somatic.learning.architecture

org.campagnelab.dl.somatic.learning.architecture.org.campagnelab.dl.somatic.learning.architecture.AbstractNeuralNetAssembler

org.campagnelab.dl.somatic.learning.architecture.org.campagnelab.dl.somatic.learning.architecture.CalibrationAssembler

org.campagnelab.dl.somatic.learning.architecture.org.campagnelab.dl.somatic.learning.architecture.EStatusListener

org.campagnelab.dl.somatic.learning.architecture.org.campagnelab.dl.somatic.learning.architecture.SixDenseLayers

org.campagnelab.dl.somatic.learning.architecture.org.campagnelab.dl.somatic.learning.architecture.SixDenseLayersForGPU

org.campagnelab.dl.somatic.learning.architecture.org.campagnelab.dl.somatic.learning.architecture.SixDenseLayersNarrower

org.campagnelab.dl.somatic.learning.architecture.org.campagnelab.dl.somatic.learning.architecture.SixDenseLayersNarrower2

org.campagnelab.dl.somatic.learning.architecture.org.campagnelab.dl.somatic.learning.architecture.SixDenseLayersNarrower2BatchNormalization

org.campagnelab.dl.somatic.learning.architecture.org.campagnelab.dl.somatic.learning.architecture.SixDenseLayersNarrower3

org.campagnelab.dl.somatic.learning.architecture.org.campagnelab.dl.somatic.learning.architecture.ThreeDenseLayers

org.campagnelab.dl.somatic.learning.architecture.graphs

org.campagnelab.dl.somatic.learning.architecture.graphs.org.campagnelab.dl.somatic.learning.architecture.graphs.SixDenseLayersNarrower2

org.campagnelab.dl.somatic.learning.architecture.graphs.org.campagnelab.dl.somatic.learning.architecture.graphs.SixDenseLayersNarrower2WithFrequency

org.campagnelab.dl.somatic.learning.architecture.graphs.org.campagnelab.dl.somatic.learning.architecture.graphs.SixDenseLayersNarrower2WithFrequencyAndBase

org.campagnelab.dl.somatic.learning.calibrate

org.campagnelab.dl.somatic.learning.calibrate.org.campagnelab.dl.somatic.learning.calibrate.CalibrateModelOutput

org.campagnelab.dl.somatic.learning.calibrate.org.campagnelab.dl.somatic.learning.calibrate.CalibratingModel

org.campagnelab.dl.somatic.learning.domains

org.campagnelab.dl.somatic.learning.domains.org.campagnelab.dl.somatic.learning.domains.IsBaseMutatedInterpreter

org.campagnelab.dl.somatic.learning.domains.org.campagnelab.dl.somatic.learning.domains.SomaticFrequencyInterpreter

org.campagnelab.dl.somatic.learning.domains.org.campagnelab.dl.somatic.learning.domains.SomaticMutationDomainDescriptor

org.campagnelab.dl.somatic.learning.domains.predictions

org.campagnelab.dl.somatic.learning.domains.predictions.org.campagnelab.dl.somatic.learning.domains.predictions.IsMutatedBasePrediction

org.campagnelab.dl.somatic.learning.domains.predictions.org.campagnelab.dl.somatic.learning.domains.predictions.IsMutatedPrediction

org.campagnelab.dl.somatic.learning.domains.predictions.org.campagnelab.dl.somatic.learning.domains.predictions.IsSomaticMutationInterpreter

org.campagnelab.dl.somatic.learning.domains.predictions.org.campagnelab.dl.somatic.learning.domains.predictions.SomaticFrequencyPrediction

org.campagnelab.dl.somatic.learning.features

org.campagnelab.dl.somatic.learning.features.org.campagnelab.dl.somatic.learning.features.Features

org.campagnelab.dl.somatic.learning.iterators

org.campagnelab.dl.somatic.learning.iterators.org.campagnelab.dl.somatic.learning.iterators.BaseInformationConcatIterator

org.campagnelab.dl.somatic.learning.iterators.org.campagnelab.dl.somatic.learning.iterators.BaseInformationIterator

org.campagnelab.dl.somatic.learning.iterators.org.campagnelab.dl.somatic.learning.iterators.CachedConcatIterator

org.campagnelab.dl.somatic.learning.iterators.org.campagnelab.dl.somatic.learning.iterators.FirstNIterator

org.campagnelab.dl.somatic.learning.iterators.org.campagnelab.dl.somatic.learning.iterators.MultiDataSetRecordIterator

org.campagnelab.dl.somatic.learning.iterators.org.campagnelab.dl.somatic.learning.iterators.NamedCachingDataSetIterator

org.campagnelab.dl.somatic.learning.iterators.org.campagnelab.dl.somatic.learning.iterators.NamedDataSetIterator

org.campagnelab.dl.somatic.learning.iterators.org.campagnelab.dl.somatic.learning.iterators.SBIRecordIterator

org.campagnelab.dl.somatic.learning.iterators.org.campagnelab.dl.somatic.learning.iterators.SamplingDataset

org.campagnelab.dl.somatic.learning.iterators.org.campagnelab.dl.somatic.learning.iterators.SamplingIterator

org.campagnelab.dl.somatic.learning.performance

org.campagnelab.dl.somatic.learning.performance.org.campagnelab.dl.somatic.learning.performance.MeasurePerformance

org.campagnelab.dl.somatic.mappers

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.AbstractFeatureMapper

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.BamFlagMapper

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.BinaryFeatureMapper

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.CategoryFeatureMapper

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.DensityMapper

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.DensityMapperCapped

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.FeatureMapperFT

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.FeatureMapperV10

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.FeatureMapperV11

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.FeatureMapperV12

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.FeatureMapperV13

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.FeatureMapperV14

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.FeatureMapperV15

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.FeatureMapperV16

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.FeatureMapperV17

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.FeatureMapperV18

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.FeatureMapperV19

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.FeatureMapperV2

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.FeatureMapperV20

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.FeatureMapperV21

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.FeatureMapperV22

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.FeatureMapperV23

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.FeatureMapperV24

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.FeatureMapperV25

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.FeatureMapperV3

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.FeatureMapperV3S

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.FeatureMapperV3SOld

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.FeatureMapperV4

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.FeatureMapperV5

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.FeatureMapperV6

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.FeatureMapperV7

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.FeatureMapperV8

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.FeatureMapperV9

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.FeatureMapperV9_2

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.FeatureMapperVT

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.FlipSamplesFeatureMapper

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.FractionDifferences

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.FractionDifferences2

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.FractionDifferences3

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.FractionDifferences4

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.FractionGenotypeCount

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.GenomicContextMapper

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.GenomicPositionDiscreteMapper

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.GenomicPositionMapper

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.GenotypeCount

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.IndelFeatures

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.IndelGenotypeCount

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.IsBaseMutatedMapper

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.IsSomaticMutationMapper

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.MagnitudeFeatures

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.MagnitudeFeatures2

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.MagnitudeFeatures3

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.MappingFunctions

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.NamingConcatFeatureMapper

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.NoMasksLabelMapper

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.PositiveControlFeatureMapper

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.QualityFeatures

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.QualityGenotypeCount

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.ReadIndexFeatures

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.ReadIndexFeaturesFix

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.ReadIndexWithCounts

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.SimpleFeatureCalculator

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.SomaticFrequencyLabelMapper

org.campagnelab.dl.somatic.mappers.org.campagnelab.dl.somatic.mappers.SortedGenotypeAgreementMapper

org.campagnelab.dl.somatic.mappers.functional

org.campagnelab.dl.somatic.mappers.functional.org.campagnelab.dl.somatic.mappers.functional.TraversalHelper

org.campagnelab.dl.somatic.mappers.trio

org.campagnelab.dl.somatic.mappers.trio.org.campagnelab.dl.somatic.mappers.trio.AbstractFeatureMapperTrio

org.campagnelab.dl.somatic.mappers.trio.org.campagnelab.dl.somatic.mappers.trio.FeatureMapperV18Trio

org.campagnelab.dl.somatic.mappers.trio.org.campagnelab.dl.somatic.mappers.trio.FeatureMapperV25Trio

org.campagnelab.dl.somatic.mappers.trio.org.campagnelab.dl.somatic.mappers.trio.FractionDifferences4Trio

org.campagnelab.dl.somatic.mappers.trio.org.campagnelab.dl.somatic.mappers.trio.IndelFeaturesTrio

org.campagnelab.dl.somatic.mappers.trio.org.campagnelab.dl.somatic.mappers.trio.MagnitudeFeatures2Trio

org.campagnelab.dl.somatic.mappers.trio.org.campagnelab.dl.somatic.mappers.trio.ReadIndexFeaturesTrio

org.campagnelab.dl.somatic.mappers.trio.org.campagnelab.dl.somatic.mappers.trio.SimpleFeatureCalculatorTrio

org.campagnelab.dl.somatic.predictions

org.campagnelab.dl.somatic.predictions.org.campagnelab.dl.somatic.predictions.DLSomaticPredictor

org.campagnelab.dl.somatic.predictions.org.campagnelab.dl.somatic.predictions.SomaticModel

org.campagnelab.dl.somatic.storage

org.campagnelab.dl.somatic.storage.org.campagnelab.dl.somatic.storage.DownSampler

org.campagnelab.dl.somatic.storage.org.campagnelab.dl.somatic.storage.DualReader

org.campagnelab.dl.somatic.storage.org.campagnelab.dl.somatic.storage.FeatureCollector

org.campagnelab.dl.somatic.storage.org.campagnelab.dl.somatic.storage.ProtobufPrinter

org.campagnelab.dl.somatic.storage.org.campagnelab.dl.somatic.storage.RecordIterable

org.campagnelab.dl.somatic.storage.org.campagnelab.dl.somatic.storage.RecordReader

org.campagnelab.dl.somatic.storage.org.campagnelab.dl.somatic.storage.RecordReaderI

org.campagnelab.dl.somatic.storage.org.campagnelab.dl.somatic.storage.RecordSpliterator

org.campagnelab.dl.somatic.storage.org.campagnelab.dl.somatic.storage.RecordWriter

org.campagnelab.dl.somatic.tools

org.campagnelab.dl.somatic.tools.org.campagnelab.dl.somatic.tools.AddCalls

org.campagnelab.dl.somatic.tools.org.campagnelab.dl.somatic.tools.AddCallsArguments

org.campagnelab.dl.somatic.tools.org.campagnelab.dl.somatic.tools.CombineWithGoldStandard

org.campagnelab.dl.somatic.tools.org.campagnelab.dl.somatic.tools.CombineWithGoldStandardArguments

org.campagnelab.dl.somatic.tools.org.campagnelab.dl.somatic.tools.MapFeatures

org.campagnelab.dl.somatic.tools.org.campagnelab.dl.somatic.tools.MapFeaturesS

org.campagnelab.dl.somatic.tools.org.campagnelab.dl.somatic.tools.Mutate

org.campagnelab.dl.somatic.tools.org.campagnelab.dl.somatic.tools.MutateArguments

org.campagnelab.dl.somatic.tools.org.campagnelab.dl.somatic.tools.PredictS

org.campagnelab.dl.somatic.tools.org.campagnelab.dl.somatic.tools.Print

org.campagnelab.dl.somatic.tools.org.campagnelab.dl.somatic.tools.PrintArguments

org.campagnelab.dl.somatic.tools.org.campagnelab.dl.somatic.tools.QuickConcat

org.campagnelab.dl.somatic.tools.org.campagnelab.dl.somatic.tools.Randomize

org.campagnelab.dl.somatic.tools.org.campagnelab.dl.somatic.tools.RandomizerArguments

org.campagnelab.dl.somatic.tools.org.campagnelab.dl.somatic.tools.ShowS

org.campagnelab.dl.somatic.tools.org.campagnelab.dl.somatic.tools.Simplify

org.campagnelab.dl.somatic.tools.org.campagnelab.dl.somatic.tools.SimplifyArguments

org.campagnelab.dl.somatic.tools.org.campagnelab.dl.somatic.tools.SomaticMapFeaturesArguments

org.campagnelab.dl.somatic.tools.org.campagnelab.dl.somatic.tools.SomaticShowArguments

org.campagnelab.dl.somatic.tools.org.campagnelab.dl.somatic.tools.Split

org.campagnelab.dl.somatic.tools.org.campagnelab.dl.somatic.tools.SplitArguments

org.campagnelab.dl.somatic.tools.org.campagnelab.dl.somatic.tools.SplitByChromosome

org.campagnelab.dl.somatic.tools.org.campagnelab.dl.somatic.tools.SplitByChromosomeArguments

org.campagnelab.dl.somatic.util

org.campagnelab.dl.somatic.util.org.campagnelab.dl.somatic.util.ErrorRecord

org.campagnelab.dl.somatic.util.org.campagnelab.dl.somatic.util.GenomicSitesVisited

org.campagnelab.dl.somatic.util.org.campagnelab.dl.somatic.util.HitBoundedPriorityQueue

org.campagnelab.dl.somatic.utils

org.campagnelab.dl.somatic.utils.org.campagnelab.dl.somatic.utils.BayesCalibrator

org.campagnelab.dl.somatic.utils.org.campagnelab.dl.somatic.utils.CalcCalibrator

org.campagnelab.dl.somatic.utils.org.campagnelab.dl.somatic.utils.FDREstimator

org.campagnelab.dl.somatic.utils.org.campagnelab.dl.somatic.utils.ProtoPredictor

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