Here is a list of all files with brief descriptions:

[detail level 1234567]

▼ java
▼ broad
▼ core
► annotation
AnnotationFactory.java
AnnotationFactoryFactory.java
AnnotationHandler.java
AnnotationReader.java
AnnotationReaderFactory.java
AnnotationUtils.java
BasicAnnotationReader.java
BasicGenomicAnnotation.java
BasicGenomicAnnotationReader.java
BasicLightweightAnnotation.java
BasicTwoSubjectAnnotation.java
BED.java
BEDGraph.java
BEDGraphReader.java
BEDReader.java
Feature.java
GenomicAnnotation.java
GenomicAnnotationFilter.java
GFF.java
GFFReader.java
LightweightGenomicAnnotation.java
MaximumContiguousSubsequence.java
RepeatMaskerAnnotation.java
RepeatMaskerAnnotationReader.java
ShortBED.java
ShortBEDReader.java
TwoSubjectAnnotation.java
► datastructures
GenericRootedTree.java
IllegalTreeOperationException.java
Interval.java
IntervalTree.java
JCSCache.java
MatrixWithHeaders.java
MatrixWithHeaderUtils.java
Pair.java
ReversibleIterator.java
► error
ParseException.java
► hmm
BadModelException.java
MarkovModel.java
MarkovState.java
► math
ANOVA.java
CombinationGenerator.java
ComputeFDR.java
Distribution.java
EmpiricalDistribution.java
FDRDistribution.java
FisherCombinedProbabilityTest.java
KSTest.java
Loess.java
MannWhitney.java
MannWhitneyPermutations.java
MathUtil.java
PermutationDistribution.java
ScanStatistics.java
Statistics.java
UnfairDie.java
Wilcox2Sample.java
► motif
► meme
AMEResultReader.java
MemeMotif.java
MemeResultReader.java
► misc
ComputeConservedMotifs.java
ScoreMotifInstances.java
PositionWeightColumn.java
PositionWeightMatrix.java
PositionWeightMatrixIO.java
PWMUtils.java
SearchException.java
SequenceMotif.java
SequenceMotifCluster.java
► multiplealignment
AlignmentExtractor.java
FastaMultipleAlignmentIO.java
MAFAlignment.java
MAFIO.java
MultipleAlignment.java
MultipleAlignmentFactory.java
MultipleAlignmentIO.java
MultipleAlignmentIOFactory.java
PhylipInterleavedMultipleAlignmentIO.java
PhylipSequencialMultipleAlignmentIO.java
► overlaputils
GeneSetIntersect.java
► parser
CommandLineParser.java
StringParser.java
► primer3
ComputeMIRScore.java
ComputeOriginalScore.java
CrossJunctionPCRDesigner.java
HairpinKmer.java
isPCRLike.java
Primer3Exception.java
Primer3PickingSummary.java
Primer3PrimerPickingResult.java
PrimerUtils.java
RestrictionEnzyme.java
► sequence
AbstractFastaParser.java
Extractor.java
FastaHandler.java
FastaParser.java
FastaQualityBinaryIO.java
FastaQualityHandler.java
FastaQualityIndex.java
FastaQualityParser.java
FastaSequenceIO.java
Sequence.java
SequenceRegion.java
SequenceRegionWindow.java
SequenceUtils.java
TranscribedRegions.java
TranscribedSequenceComposition.java
WindowSlider.java
► siphy
► tools
► conservation
AverageBranchLength.java
BatchSubmitEstimateExon.java
ComputeKmersForRegion.java
ComputeMaxPercentileOfElements.java
ComputePercentageOfKmers.java
EstimateOmegaPerExon.java
SplitFile.java
ConservationUtils.java
ConservedPWMScanner.java
EvolutionaryModel.java
EvolutionaryModelParameters.java
Fit.java
PhastconsReader.java
PiHMM.java
PositionWeightMatrixModel.java
ScaledWindowParserListener.java
StationaryDistributionIO.java
TreeScaler.java
TreeScalerIO.java
UnableToFitException.java
► util
ChromosomeStringComparator.java
CLUtil.java
CollapseByIntersection.java
GMTParser.java
ParseGCTFile.java
▼ pda
► annotation
BEDFileParser.java
GTFFileParser.java
Locus.java
► countreads
AnnotationCounts.java
FastqLibraryStats.java
► datastructures
Alignments.java
AlignmentsReader.java
LocationAwareMatrix.java
► differentialExpression
BatchNorm.java
CisVsTrans.java
CollapseProjections.java
ConvertToDiscreteMatrix.java
DifferentialExpression.java
DifferentialScoring.java
FixedControlDifferentialExpression.java
FoldSignificance.java
FWERDistribution.java
GrabProbes.java
GSAProjection.java
MakePositionalGeneSets.java
MergeGSEAOutputIntoMatrix.java
Permutations.java
RunAllGSEABatch.java
RunDifferentialExpression.java
RunGSEA.java
RunTimeSeries.java
SplitByName.java
► enrichment
EnrichmentMetric.java
EnrichmentUtils.java
► feature
► genome
Chromosome.java
DirectoryInstalledGenomeAssembly.java
► gene
functionalAnnotation.java
GeneTools.java
GeneWithIsoforms.java
NeighborAnalysis.java
NeighborsNullModel.java
transcriptsNullModel.java
► geneexpression
► agilent
► analysis
ProcessDataset.java
AgilentArrayStats.java
AgilentProbe.java
AgilentToGCT.java
AgilentUtils.java
ClassifyAgilentLincProbes.java
CollapseProbesByMinPValue.java
CorrelationAgilentNanostring.java
CorrelationBetweenReplicates.java
ExtractSamplesAndLabel.java
FilterMatrixByMinCutoff.java
FindProbesForGeneSet.java
MakeCLSFiles.java
MakeCLSFromDescription.java
QCAgilentResults.java
► clustering
AbsolutePearsonFunction.java
Cluster.java
ClusterDistanceFunction.java
ComputeCorrelationOfReplicates.java
CorrelationMatrix.java
EuclideanDistance.java
HierarchicalClustering.java
Kmeans.java
PearsonDistance.java
RankOrder.java
ComputeHypergeomtricEnrichment.java
CountNums.java
ExpressionExperimentInfo.java
FilterGCT.java
FilterGCTFile.java
geneExpUtils.java
GlobalStats.java
GrabSpecificColumns.java
PaGEJava.java
PreprocessDataSet.java
ScoreDiffGenes.java
► rap
► misc
FindEnrichedDepletedRegions.java
► rnai
ExtractSequence.java
RNAiGeneAnnotation.java
► samtools
FilterFastqReads.java
FilterPairedReadsByMAQ.java
PairedEndReadIterator.java
PairedEndTDF.java
SAMFragmentWriter.java
SAMPairedEndFileReader.java
TrimFastqReads.java
WrappedIterator.java
► seq
► alignment
AlignmentUtils.java
StoredAlignmentStats.java
► chip
ComputeEnrichments.java
FindDiffrentialEnrichedRegions.java
PeakFilter.java
► clip
FastaExtendPeaks.java
GenomeSpaceSampleData.java
Pileup.java
SampleData.java
► fastq
FastqParser.java
FastqSequence.java
FastqSplitterByBarcode.java
SplitAndTrimIndex.java
SplitFastqByIndex.java
► graph
ChromosomeWithBubblesJGraphT.java
Path.java
► protection
BatchedMultiSampleScanPeakCaller.java
GenomeSpaceSampleData.java
MultiSampleScanPeakCaller.java
ReadSimulator.java
ReadSimulator2.java
SampleData.java
TwoSampleScanSkellamPeakCaller.java
WindowScores.java
► rap
► rna
CollectRnaSeqMetrics.java
CountReads.java
TranscriptomeCommandLineProgram.java
TranscriptomeScoringProgram.java
BuildRatioNullDistribution.java
CalculateCoverageStats.java
CollectAnnotationEnrichments.java
CountProbes.java
CountReads.java
DistanceToBED.java
GCContent.java
GenomeCommandLineProgram.java
GenomeScoringProgram.java
PlotAggregateRegions.java
RAPPeakCaller.java
RatioPermutationPeakCaller.java
ShuffleBAM.java
ShuffleBED.java
SkellamKLPeakCaller.java
SkellamScore.java
SlideAndCalculate.java
SlideAndCount.java
UnmarkDuplicates.java
► segmentation
► utils
ReconstructionComparer.java
AlignmentDataModel.java
AlignmentDataModelStats.java
ContinuousDataAlignmentModel.java
DefineSourceAndSinkFromPairedEnds.java
GeneCounts.java
GenericAlignmentDataModel.java
GeneScore.java
GenomeWithGaps.java
GenomeWithGaps2.java
GlobalSpliceFilter.java
PrecomputeDataAlignmentStats.java
ReadCountNormalizer.java
ReadFilter.java
WrappedIGVIterator.java
► tools
PSLXToSAM.java
▼ projection
► gsa
DefineGeneSignatures.java
ExtractGenes.java
GeneSetEnrichment.java
GSAScoring.java
GsaUtils.java
▼ jaligner
▼ formats
CLUSTAL.java
FASTA.java
Format.java
FormatFactory.java
Pair.java
▼ matrix
MatricesCompartor.java
Matrix.java
MatrixGenerator.java
MatrixLoaderException.java
▼ util
Commons.java
SequenceParser.java
SequenceParserException.java
Alignment.java
Cell.java
Directions.java
Markups.java
NeedlemanWunsch.java
NeedlemanWunschGotoh.java
Sequence.java
SmithWatermanGotoh.java
TracebackNode.java
▼ Jama
▼ util
Maths.java
CholeskyDecomposition.java
EigenvalueDecomposition.java
LUDecomposition.java
Matrix.java
QRDecomposition.java
SingularValueDecomposition.java
▼ umms
▼ core
► alignment
AbstractPairedEndAlignment.java
Alignment.java
AlignmentPair.java
ChromosomeInconsistencyException.java
FeatureSequenceAlignment.java
FragmentAlignment.java
PairedEndAlignmentFactory.java
PairedReadAlignment.java
SingleEndAlignment.java
SmatchLike.java
SmithWatermanAlignment.java
► annotation
► filter
FullyContainedFilter.java
OverlapFilter.java
AbstractAnnotation.java
AbstractAnnotationCollection.java
Annotation.java
AnnotationCollection.java
AnnotationFileReader.java
AnnotationList.java
BasicAnnotation.java
CompoundInterval.java
Gene.java
PSLRecord.java
SingleInterval.java
► coordinatesystem
AnnotationOutOfBoundsException.java
CoordinateSpace.java
GenomicSpace.java
MaskedGenomicSpace.java
PermutationNotFoundException.java
ShuffledIterator.java
TranscriptInGenomicSpace.java
TranscriptomeSpace.java
► exception
IncompleteMethodImplementationException.java
RuntimeIOException.java
► feature
GeneWindow.java
GenomeWindow.java
Window.java
► general
CloseableFilterIterator.java
Predicates.java
TabbedReader.java
► model
► score
AbstractListScore.java
BasicScanStatisticScore.java
BinomialEnrichmentScore.java
CountScore.java
CoverageScore.java
EndInWindowCountScore.java
LengthScore.java
MultiScore.java
NewRatioScore.java
PoissonEnrichmentScore.java
RatioScore.java
ScanStatisticScore.java
StartInWindowCountScore.java
SumScore.java
WindowAllScore.java
WindowProcessor.java
WindowScore.java
WindowScoreIterator.java
AlignmentModel.java
JCSAlignmentModel.java
► readers
PairedEndReader.java
► readFilters
GenomicSpanFilter.java
MappingQualityFilter.java
PairedAndProperFilter.java
PairedEndFilter.java
PCRDuplicateFilter.java
ReadEndsInFilter.java
ReadStartsInFilter.java
ReadsToReconstructFilter.java
SameOrientationFilter.java
SplicedReadFilter.java
UniqueMappedReadsFilter.java
► scripture
► statistics
ConnectDisconnectedTranscripts.java
BuildScriptureCoordinateSpace.java
OrientedChromosomeTranscriptGraph.java
► utils
AnnotationUtils.java
► writers
PairedEndWriter.java
▼ esat
CollapsedGeneLengths.java
ESAT.java
ESATDistanceCalculator.java