├── .classpath ├── .gitignore ├── .pmd ├── .project ├── Genomes └── genomes_folder.txt ├── Help ├── 1 Introduction │ ├── 1.1 What is SeqMonk.html │ └── 1.2 Terminology.html ├── 2 Opening a Project │ ├── 2.1 Opening an Existing Project.html │ └── 2.2 Starting a New Project │ │ ├── 2.2 Starting a New Project.html │ │ ├── 2.2.1 Selecting a Genome.html │ │ ├── 2.2.2 Importing Data │ │ ├── 2.2.2 Importing Data.html │ │ ├── 2.2.2.1 BED Files.html │ │ ├── 2.2.2.10 Importing Probes as Data.html │ │ ├── 2.2.2.3 Bowtie Files.html │ │ ├── 2.2.2.4 Eland Files.html │ │ ├── 2.2.2.5 GFF Files.html │ │ ├── 2.2.2.6 Maq Files.html │ │ ├── 2.2.2.7 SAM or BAM Files.html │ │ ├── 2.2.2.8 Generic Text Files.html │ │ ├── 2.2.2.9 Reimporting Existing Data.html │ │ ├── bowtie_options.png │ │ ├── edit_data_sets.png │ │ ├── eland_options.png │ │ ├── import_warnings.png │ │ ├── maq_options.png │ │ ├── reimport_options.png │ │ ├── sam_options.png │ │ └── text_file_import.png │ │ ├── 2.2.3 Grouping Samples.html │ │ ├── 2.2.4 Importing Extra Annotation │ │ ├── 2.2.4 Importing Extra Annotation.html │ │ ├── 2.2.4.1 Importing Annotation from GFF or GTF Files.html │ │ ├── 2.2.4.2 Importing Annotation from a Probe List.html │ │ ├── 2.2.4.3 Importing Annotation from Generic Text Files.html │ │ ├── annotation_sets_folder.png │ │ └── generic_text_import_annotation.png │ │ ├── auto_split_options.png │ │ ├── data_groups.png │ │ ├── genome_selector.png │ │ └── remote_genome_selector.png ├── 3 Visualisation │ ├── 3.1 The Main Display │ │ ├── 3.1 The Main Display.html │ │ ├── 3.1.1 The Data View.html │ │ ├── 3.1.2 The Genome View.html │ │ ├── 3.1.3 The Chromosome View.html │ │ ├── 3.1.4 The Toolbar.html │ │ ├── 3.1.5 The Status Bar.html │ │ ├── chromosome_view.png │ │ ├── data_track_display_options.png │ │ ├── data_view.png │ │ ├── data_view_datastore_popup.png │ │ ├── data_zoom_level.png │ │ ├── feature_annotation.png │ │ ├── genome_view.png │ │ ├── main_display.png │ │ ├── probe_list_view.png │ │ ├── set_annotation_tracks.png │ │ ├── set_data_tracks.png │ │ ├── status_bar.png │ │ ├── toolbar_change_density.png │ │ ├── toolbar_change_packing.png │ │ ├── toolbar_change_tracks.png │ │ ├── toolbar_data_zoom.png │ │ ├── toolbar_display_type.png │ │ ├── toolbar_origin_options.png │ │ ├── toolbar_search.png │ │ └── whole_toolbar.png │ ├── 3.2 Figures and Graphs │ │ ├── 3.2 Figures and Graphs.html │ │ ├── 3.2.1 The BoxWhisker Plot.html │ │ ├── 3.2.10 The Correlation Matrix.html │ │ ├── 3.2.11 The Cumulative Distribution Plot.html │ │ ├── 3.2.12 The HiC Heatmap Plot.html │ │ ├── 3.2.13 The MA Plot.html │ │ ├── 3.2.14 The HiC Length Histogram.html │ │ ├── 3.2.15 The Hierarchical Cluster Plot.html │ │ ├── 3.2.16 The HiC Cis-Trans Scatterplot.html │ │ ├── 3.2.17 The Domainogram Plot.html │ │ ├── 3.2.18 The Quantitation Trend Plot.html │ │ ├── 3.2.19 The Probe List Overlap Matrix.html │ │ ├── 3.2.2 The DataStore Tree.html │ │ ├── 3.2.20 The Star Wars Plot.html │ │ ├── 3.2.22 The RNA-Seq QC Plot.html │ │ ├── 3.2.23 The Small RNA QC Plot.html │ │ ├── 3.2.24 The Variation Plot.html │ │ ├── 3.2.25 The Bean Plot.html │ │ ├── 3.2.25 The PCA Plot.html │ │ ├── 3.2.26 The TSNE Plot.html │ │ ├── 3.2.27 The Strand Bias Plot.html │ │ ├── 3.2.27 The Volcano Plot.html │ │ ├── 3.2.3 The Probe Value Histogram.html │ │ ├── 3.2.4 The Probe Length Histogram.html │ │ ├── 3.2.5 The Reading Length Histogram.html │ │ ├── 3.2.6 The Probe Trend Plot.html │ │ ├── 3.2.7 The Aligned Probes Plot.html │ │ ├── 3.2.8 The Scatter Plot.html │ │ ├── 3.2.9 The Line Graph.html │ │ ├── aligned_probes_plot.png │ │ ├── aligned_probes_preferences.png │ │ ├── bean_plot.png │ │ ├── boxwhisker_plot.png │ │ ├── correlation_matrix.png │ │ ├── datastore_tree.png │ │ ├── distribution_plot.png │ │ ├── domainogram.png │ │ ├── domainogram_options.png │ │ ├── hic_cis-trans_scatterplot.png │ │ ├── hic_heatmap.png │ │ ├── hic_heatmap_options.png │ │ ├── hic_length_histogram.png │ │ ├── hierarchical_clusters.png │ │ ├── line_graph.png │ │ ├── ma_plot.png │ │ ├── pca_plot.png │ │ ├── pca_variances.png │ │ ├── probe_list_overlap_matrix.png │ │ ├── probe_trend_plot.png │ │ ├── probe_trend_preferences.png │ │ ├── probe_value_histogram.png │ │ ├── quantitation_trend_options.png │ │ ├── quantitation_trend_plot.png │ │ ├── rna_seq_qc_options.png │ │ ├── rna_seq_qc_plot.png │ │ ├── scatter_plot.png │ │ ├── scatter_plot_sublists.png │ │ ├── small_rna_qc_options.png │ │ ├── small_rna_qc_plot.png │ │ ├── starwars_plot.png │ │ ├── strand_bias_plot.png │ │ ├── tsne_plot.png │ │ ├── variation_plot.png │ │ └── volcano_plot.png │ ├── 3.3 Movement Controls.html │ ├── 3.4 Searching.html │ ├── after_zooming.png │ ├── find_features.png │ ├── goto_position.png │ ├── goto_window.png │ └── whilst_zooming.png ├── 4 Quantitation │ ├── 4 Quantitation.html │ ├── 4.1 Probe Generators │ │ ├── 4.1.1 Running Window Probe Generator.html │ │ ├── 4.1.10 Merge Consecutive Probe Generator.html │ │ ├── 4.1.11 MACS Peak Caller Probe Generator.html │ │ ├── 4.1.12 Random Probe Generator.html │ │ ├── 4.1.13 Shuffle Existing List Probe Generator.html │ │ ├── 4.1.14 Even Coverage Probe Generator.html │ │ ├── 4.1.2 Contig Probe Generator.html │ │ ├── 4.1.3 Feature Probe Generator.html │ │ ├── 4.1.4 Feature Percentile Probe Generator.html │ │ ├── 4.1.5 Create Probes from Existing List Generator.html │ │ ├── 4.1.6 Interstitial Probe Generator.html │ │ ├── 4.1.7 Deduplication Probe Generator.html │ │ ├── 4.1.8 Read Position Probe Generator.html │ │ ├── 4.1.9 Current Region Probe Generator.html │ │ ├── contig_generator.png │ │ ├── contig_probe_generator.png │ │ ├── deduplication_probe_generator.png │ │ ├── even_coverage_probe_generator.png │ │ ├── feature_generator.png │ │ ├── feature_percentile_generator.png │ │ ├── interstitial_probe_generator.png │ │ ├── macs_options.png │ │ ├── merge_consecutive_probe_generator.png │ │ ├── read_position_probe_generator.png │ │ └── running_window_generator.png │ ├── 4.2 Quantitation Methods │ │ ├── 4.2.1 Read Count Quantitation.html │ │ ├── 4.2.10 Per Probe Normalisation Quantitation.html │ │ ├── 4.2.11 Exact Overlap Quantitation.html │ │ ├── 4.2.12 Z-Score Quantitation.html │ │ ├── 4.2.13 Match Distribution Quantitation.html │ │ ├── 4.2.14 Fixed Value Quantitation.html │ │ ├── 4.2.15 HiC Read Count Quantitation.html │ │ ├── 4.2.16 HiC Trans Cis Quantitation.html │ │ ├── 4.2.17 HiC Prev Next Quantitation.html │ │ ├── 4.2.18 HiC PCA Domain Quantitation.html │ │ ├── 4.2.19 4C Enrichment Quantitation.html │ │ ├── 4.2.2 Base Pair Quantitation.html │ │ ├── 4.2.20 Distance to Feature Quantitation.html │ │ ├── 4.2.21 Smoothing Quantitation.html │ │ ├── 4.2.22 Probe Length Quantitation.html │ │ ├── 4.2.23 Smoothing Subtraction Quantitation.html │ │ ├── 4.2.24 Log Transform Quantitation.html │ │ ├── 4.2.25 Subset Normalisation Quantitation.html │ │ ├── 4.2.26 Enrichment Normalisation Quantitation.html │ │ ├── 4.2.27 Linear Regression Normalisation Quantitation.html │ │ ├── 4.2.28 Duplication Quantitation.html │ │ ├── 4.2.29 Strand Bias Quantitation.html │ │ ├── 4.2.3 Enrichment Quantitation.html │ │ ├── 4.2.4 Difference Quantitation.html │ │ ├── 4.2.5 Coverage Depth Quantitation.html │ │ ├── 4.2.6 Percentage Coverage Quantitation.html │ │ ├── 4.2.7 Relative Quantitation.html │ │ ├── 4.2.8 Manual Correction Quantitation.html │ │ ├── 4.2.9 Percentile Normalisation Quantitation.html │ │ ├── 4.2.9 Rank Quantitation.html │ │ ├── Coverage Depth Quantitationpic.png │ │ ├── base_pair_quantitation.png │ │ ├── coverage_depth_quantitation.png │ │ ├── difference_quantitationpic.png │ │ ├── distance_to_feature_quantitation.png │ │ ├── exact_overlap_count_quantitiation.png │ │ ├── hic_pca_domain_quantitation.png │ │ ├── hic_prev_next_quantitation.png │ │ ├── hic_read_count_quantitation.png │ │ ├── hic_trans_cis_quantitation.png │ │ ├── manual_correction_quantitation.png │ │ ├── percent_coverage_quantitation.png │ │ ├── percentile_normalisation_quantitation.png │ │ ├── read_count_quanititation.png │ │ └── z_score_quantitation.png │ ├── 4.3 Pipelines │ │ ├── 4.3.1 RNA-Seq quantitation pipeline.html │ │ ├── 4.3.2 Wiggle pipeline.html │ │ ├── 4.3.3 Bisulphite feature methylation pipeline.html │ │ ├── 4.3.4 Splicing Efficiency pipeline.html │ │ ├── 4.3.5 Antisense Transcription pipeline.html │ │ ├── 4.3.6 Genetrap quantitation pipeline.html │ │ ├── 4.3.7 Active transcription quantitation pipeline.html │ │ ├── 4.3.8 Transcription termination quantitation pipeline.html │ │ ├── bsseq_options.png │ │ ├── genetrap_options.png │ │ ├── rpkm_options.png │ │ ├── splicing_efficiency_options.png │ │ ├── splicing_efficiency_quantitiation.PNG │ │ └── termination_options.png │ ├── define_probes.png │ └── quantitation_options.png ├── 5 Filtering │ ├── 5 Filtering.html │ ├── 5.1 Value Filters │ │ ├── 5.1.1 Individual Probe Value Filter.html │ │ ├── 5.1.2 Windowed Value Filter.html │ │ ├── 5.1.3 Individual Probe Value Difference Filter.html │ │ ├── 5.1.4 Windowed Value Difference Filter.html │ │ ├── 5.1.5 Value Distribution Filter.html │ │ ├── individual_probe_value_difference_options.png │ │ ├── individual_probe_value_options.png │ │ ├── value_distribution_filter_options.png │ │ ├── windowed_probe_value_difference_options.png │ │ └── windowed_value_options.png │ ├── 5.2 Statistical Filters │ │ ├── 5.2.1 BoxWhisker Filter.html │ │ ├── 5.2.2 Windowed Replicate Filter.html │ │ ├── 5.2.3 Replicate Set Filter.html │ │ ├── 5.2.4 Intensity Difference Filter.html │ │ ├── 5.2.6 Monte Carlo Filter.html │ │ ├── 5.2.7 Chi Square Filter.html │ │ ├── 5.2.8 Binomial Filter.html │ │ ├── 5.2.9 Proportion of Library Filter.html │ │ ├── boxwhisker_filter_options.png │ │ ├── replicate_filter_options.png │ │ └── replicate_set_filter_options.png │ ├── 5.3 R Statistical Filters │ │ ├── 5.3.1 DESeq2 Filter.html │ │ ├── 5.3.2 EdgeR Filter.html │ │ ├── 5.3.4 EdgeR for-rev Filter.html │ │ ├── 5.3.4 Logistic Regression Filter.html │ │ └── 5.3.5 Logistic Regression Splicing Filter.html │ ├── 5.4 Correlation Filters │ │ ├── 5.4.1 Correlation Cluster Filter.html │ │ ├── 5.4.2 Probe List Correlation Filter.html │ │ ├── 5.4.3 Manual Probe Correlation Filter.html │ │ └── manual_correlation.png │ ├── 5.5 Manging Probe Lists.html │ ├── 5.5 Variance Filters │ │ ├── 5.5.1 Individual Replicate Set Variance Filter.html │ │ └── individual_probe_variance_options.png │ ├── 5.6 Other Filters │ │ ├── 5.6.1 Feature Filter.html │ │ ├── 5.6.10 Segmentation Filter.html │ │ ├── 5.6.11 Duplicate List Filter.html │ │ ├── 5.6.2 Position Filter.html │ │ ├── 5.6.3 Probe Length Filter.html │ │ ├── 5.6.5 Random Probes Filter.html │ │ ├── 5.6.7 Deduplication Filter.html │ │ ├── 5.6.8 Feature Name Filter.html │ │ ├── 5.6.9 Probe Name Filter.html │ │ ├── deduplication_filter_options.png │ │ ├── feature_filter_options.png │ │ ├── feature_name_filter_options.png │ │ └── position_filter_options.png │ └── 5.7 List Intersection Filters │ │ ├── 5.7.1 Logically Combine Existing Lists.html │ │ ├── 5.7.2 Collate Existing Lists.html │ │ ├── 5.7.3 Intersect Existing Lists.html │ │ └── combine_list_options.png ├── 6 Reports │ ├── 6.1 The Annotated Probe Report.html │ ├── 6.2 The Probe Group Report.html │ ├── 6.3 The Feature Report.html │ ├── 6.4 The DataStore Summary Report.html │ ├── 6.5 The Probe List Description Report.html │ ├── 6.6 Vistories.html │ ├── annotated_probe_report.png │ ├── annotated_probe_report_options.png │ ├── feature_report.png │ ├── feature_report_options.png │ ├── probe_group_report.png │ └── probe_group_report_options.png ├── 7 Saving Data │ ├── 7.1 Saving a Project.html │ ├── 7.2 Saving Images.html │ ├── 7.3 Saving Text.html │ ├── 7.4 Saving Quantitation Annotation Tracks.html │ ├── save_before_exit.png │ └── select_image_type.png ├── 8 Configuration │ ├── 8.1 SeqMonk Preferences.html │ ├── 8.2 Memory Settings.html │ └── preferences_dialog.png └── 9 Troubleshooting │ ├── 9.1 Common Problems.html │ ├── 9.2 Reporting Bugs.html │ ├── 9.3 OSX Full Disk Access.html │ └── osx_disk_permissions.png ├── INSTALL.txt ├── Jama-1.0.2.jar ├── LICENSE ├── LICENSE.txt ├── NOTICE_FOR_COMMONS_MATH_CODE.txt ├── OSX ├── Cargo.toml ├── README_RUST_COMPILE └── src │ └── main.rs ├── README.md ├── README.txt ├── RELEASE_NOTES.txt ├── Scripts ├── build_seqmonk_release.sh ├── export_annotated_embl_from_assembly.pl ├── export_annotated_embl_from_plant_or_bacteria.pl └── setup_osx_ec2_build_environment.sh ├── SeqMonk.exe ├── Templates ├── vistory_footer.html └── vistory_header.html ├── Windows ├── SeqMonk.cs └── seqmonk.ico ├── com └── sun │ └── java │ └── TableSorter.java ├── commons-math3-3.5.jar ├── edu └── northwestern │ └── at │ └── utils │ ├── FileUtils.java │ ├── Formatters.java │ ├── PrintfFormat.java │ ├── Sorting.java │ ├── StringUtils.java │ └── math │ ├── ArithUtils.java │ ├── Complex.java │ ├── Constants.java │ ├── DyadicFunction.java │ ├── Factorial.java │ ├── MonadicFunction.java │ ├── NumberOps.java │ ├── Polynomial.java │ ├── SplitDouble.java │ ├── distributions │ ├── Beta.java │ ├── ChiSquare.java │ ├── ErrorFunction.java │ ├── FishersF.java │ ├── Gamma.java │ ├── Normal.java │ ├── Sig.java │ ├── Studentst.java │ └── package.html │ ├── matrix │ ├── AbstractMatrix.java │ ├── CholeskyDecomposition.java │ ├── ColumnTransformation.java │ ├── ColumnTransformer.java │ ├── DenseMatrix.java │ ├── EigenvalueDecomposition.java │ ├── LUDecomposition.java │ ├── Matrices.java │ ├── MatricesMeasure.java │ ├── Matrix.java │ ├── MatrixConditionalEBETransformation.java │ ├── MatrixEBEOperation.java │ ├── MatrixEBETransformation.java │ ├── MatrixEBETransformer.java │ ├── MatrixFactory.java │ ├── MatrixFromString.java │ ├── MatrixMeasure.java │ ├── MatrixMismatchedSizeException.java │ ├── MatrixOperator.java │ ├── MatrixProperty.java │ ├── MatrixSingularException.java │ ├── MatrixToString.java │ ├── MatrixTransformer.java │ ├── QRDecomposition.java │ ├── RowTransformer.java │ ├── SingularValueDecomposition.java │ └── SparseMatrix.java │ ├── randomnumbers │ ├── MersenneTwister.java │ └── RandomVariable.java │ ├── rootfinders │ ├── Bisection.java │ ├── BracketRoot.java │ ├── Brent.java │ ├── MonadicFunctionRootFinder.java │ ├── NewtonRaphson.java │ ├── RootFinderConvergenceTest.java │ ├── RootFinderIterationInformation.java │ ├── Secant.java │ ├── StandardRootFinderConvergenceTest.java │ └── package.html │ └── statistics │ ├── ContingencyTable.java │ ├── Covar.java │ ├── Descriptive.java │ ├── FishersExactTest.java │ ├── OneWayTable.java │ ├── PrincipalComponents.java │ ├── RankOrder.java │ ├── SpearmanCorr.java │ └── Standardize.java ├── htsjdk.jar ├── net └── sourceforge │ └── iharder │ └── base64 │ └── Base64.java ├── osxseqmonk ├── seqmonk ├── seqmonk.desktop ├── seqmonk_import └── uk └── ac └── babraham └── SeqMonk ├── Analysis ├── Correlation │ ├── DistanceMatrix.java │ └── PearsonCorrelation.java └── Statistics │ ├── AnovaTest.java │ ├── BenjHochFDR.java │ ├── BoxWhisker.java │ ├── ChiSquareTest.java │ ├── FDistribution.java │ ├── IndexTTestValue.java │ ├── MappedGeneSetTTestValue.java │ ├── PCA.java │ ├── ProbeGroupTTestValue.java │ ├── ProbeTTestValue.java │ ├── SimpleStats.java │ ├── SmoothedVarianceDataset.java │ ├── StarWars.java │ ├── TDistribution.java │ └── TTest.java ├── AnnotationParsers ├── AnnotationParser.java ├── AnnotationParserRunner.java ├── GFF3AnnotationParser.java ├── GenericAnnotationParser.java ├── GenomeParser.java ├── ProbeListAnnotationParser.java └── SeqMonkAnnotationReimportParser.java ├── DataParsers ├── ActiveProbeListParser.java ├── BAMFileParser.java ├── BedFileParser.java ├── BedMethylFileParser.java ├── BedPEFileParser.java ├── BismarkCovFileParser.java ├── BowtieFileParser.java ├── DataParser.java ├── DataParserOptionsPanel.java ├── GenericSeqReadParser.java ├── GffFileParser.java ├── HiCOtherEndExtractor.java ├── MethylKitFileParser.java ├── MethylSeqFileParser.java ├── QuasRFileParser.java ├── SeqMonkDataReimportParser.java ├── SeqMonkParser.java └── VisibleStoresParser.java ├── DataTypes ├── CacheListener.java ├── Cluster │ ├── ClusterDataSource.java │ ├── ClusterPair.java │ └── HierarchicalClusterSet.java ├── DataChangeListener.java ├── DataCollection.java ├── DataGroup.java ├── DataSet.java ├── DataStore.java ├── Genome │ ├── AnnotationCollection.java │ ├── AnnotationCollectionListener.java │ ├── AnnotationSet.java │ ├── AnnotationTagValue.java │ ├── Chromosome.java │ ├── CoreAnnotationSet.java │ ├── Feature.java │ ├── Genome.java │ ├── Location.java │ ├── MultiGenome.java │ ├── SingleGenome.java │ └── SplitLocation.java ├── HiCDataStore.java ├── Interaction │ ├── HeatmapMatrix.java │ ├── HeatmapMatrixListener.java │ ├── HiCInteractionStrengthCalculator.java │ ├── InteractionClusterMatrix.java │ └── InteractionProbePair.java ├── PairedDataSet.java ├── Probes │ ├── Probe.java │ ├── ProbeList.java │ ├── ProbeSet.java │ ├── ProbeSetChangeListener.java │ └── ProbeStrandType.java ├── ProgressListener.java ├── ReplicateSet.java └── Sequence │ ├── HiCHitCollection.java │ ├── QuantitationStrandType.java │ ├── ReadStrandType.java │ ├── ReadsWithCounts.java │ ├── SequenceRead.java │ └── SequenceReadWithChromosome.java ├── DataWriters ├── BedDataWriter.java ├── BedGraphDataWriter.java └── SeqMonkDataWriter.java ├── Dialogs ├── AboutDialog.java ├── AnnotationSetEditor │ └── AnnotationSetEditor.java ├── AnnotationSetPropertiesDialog.java ├── AnnotationTrackSelector.java ├── AutoSplitDataDialog.java ├── AxisScaleEditor.java ├── Cancellable.java ├── CrashReporter │ ├── CrashReporter.java │ └── CrashReporterDialog.java ├── DataParser │ └── DataParserOptionsDialog.java ├── DataSetEditor │ ├── CollectDataSetNamesDialog.java │ ├── DataSetEditor.java │ └── MultiDataSetRenameDialog.java ├── DataStorePropertiesDialog.java ├── DataTrackSelector │ ├── DataStoreListModel.java │ └── DataTrackSelector.java ├── DataZoomSelector.java ├── EditPreferencesDialog.java ├── Filters │ └── FilterOptionsDialog.java ├── FindFeatureDialog.java ├── FindFeaturesByNameDialog.java ├── GenomeDownloadSelector.java ├── GenomeSelector.java ├── GotoDialog │ ├── GotoDialog.java │ ├── GotoWindowDialog.java │ └── RecentLocation.java ├── GroupEditor.java ├── LicenseDialog.java ├── ListOverlapsDialog.java ├── OrderedListSelector.java ├── OrderedReplicateSetSelector.java ├── ProbeListCommentEditDialog.java ├── ProbeListSelectorDialog.java ├── ProbeListViewer.java ├── ProgressDialog │ ├── CountedException.java │ ├── ProgressDialog.java │ └── WarningDisplayDialog.java ├── ProgressRecordDialog.java ├── Renderers │ ├── QuantitationTypeRenderer.java │ └── TypeColourRenderer.java ├── ReplicateSetEditor.java ├── ReplicateSetSelector.java ├── SeqMonkPreview │ ├── SeqMonkPreview.java │ └── SeqMonkPreviewPanel.java └── SimilarProbeListsDialog.java ├── Displays ├── AlignedProbePlot │ ├── AlignedSummaryDialog.java │ ├── AlignedSummaryPanel.java │ ├── AlignedSummaryPreferences.java │ ├── AlignedSummaryPreferencesDialog.java │ ├── CorrelationPair.java │ └── CorrelationSet.java ├── BeanPlot │ ├── BeanPlotPanel.java │ ├── BeanPlotScaleBar.java │ ├── MultiBeanPlotDialog.java │ └── MultiBeanPlotPanel.java ├── BoxWhisker │ ├── BoxWhiskerPanel.java │ ├── MultiBoxWhiskerDialog.java │ └── MultiBoxWhiskerPanel.java ├── ChromosomeViewer │ ├── ChromosomeDataTrack.java │ ├── ChromosomeFeatureTrack.java │ ├── ChromosomePositionScrollBar.java │ ├── ChromosomeScaleTrack.java │ ├── ChromosomeViewer.java │ ├── ChromosomeViewerLayout.java │ └── MinSizeDataTrack.java ├── CisTransScatterplot │ ├── CisTransScatterPlotDialog.java │ └── CisTransScatterPlotPanel.java ├── CodonBiasPlot │ ├── CodonBiasDialog.java │ ├── CodonBiasPanel.java │ └── SingleFeatureSelector.java ├── CorrelationMatrix │ └── CorrelationMatrix.java ├── CumulativeDistribution │ ├── CumulativeDistributionDialog.java │ └── CumulativeDistributionPanel.java ├── DataStoreTree │ ├── DataStoreClusterPanel.java │ ├── DataStoreCorrelationDataSource.java │ └── DataStoreTreeDialog.java ├── DataViewer │ ├── DataCollectionTreeModel.java │ ├── DataTreeRenderer.java │ ├── DataViewer.java │ └── ProbeSetTreeModel.java ├── DesignEditor │ ├── InvalidFactorException.java │ ├── StatisticalDesign.java │ └── StatisticalDesignEditorDialog.java ├── Domainogram │ ├── DomainogramChromosomePanel.java │ ├── DomainogramDialog.java │ └── DomainogramPreferencesDialog.java ├── DuplicationPlot │ ├── DuplicationPlotDialog.java │ ├── DuplicationPlotPanel.java │ └── RestrictedDataStoreSelector.java ├── FeatureListViewer │ └── FeatureListViewer.java ├── FeaturePositionSelector │ ├── FeaturePercentileSelectorPanel.java │ └── FeaturePositionSelectorPanel.java ├── FeatureViewer │ ├── FeatureAnnotationTableModel.java │ └── FeatureViewer.java ├── GenomeViewer │ ├── ChromosomeDisplay.java │ ├── ChromosomeScale.java │ └── GenomeViewer.java ├── GiraphPlot │ ├── GiraphPlot.java │ ├── GiraphPlotCluster.java │ ├── GiraphPlotClusterPair.java │ └── GiraphPlotPanel.java ├── GradientScaleBar │ ├── GradientPanel.java │ ├── GradientScaleAxis.java │ └── GradientScaleBar.java ├── HTMLDisplay │ └── HTMLDisplayDialog.java ├── Help │ ├── HelpDialog.java │ ├── HelpIndexRoot.java │ ├── HelpPage.java │ ├── HelpPageDisplay.java │ └── HelpSearchPanel.java ├── HiCHeatmap │ ├── HeatmapFilterOptions.java │ ├── HeatmapGenomePanel.java │ ├── HeatmapGenomePanelCollection.java │ ├── HeatmapGenomeWindow.java │ ├── HeatmapOptionsPanel.java │ ├── HeatmapPositionListener.java │ ├── HeatmapProbeListPanel.java │ ├── HeatmapProbeListPanelCollection.java │ ├── HeatmapProbeListWindow.java │ └── HiCGradientPanel.java ├── HierarchicalClusterPlot │ ├── HierarchicalClusterCorrelationDataSource.java │ ├── HierarchicalClusterDialog.java │ ├── HierarchicalClusterDistanceDataSource.java │ └── HierarchicalClusterPanel.java ├── HistogramPlot │ ├── HiCLengthHistogramPlot.java │ ├── HistogramPanel.java │ ├── ProbeLengthHistogramPlot.java │ ├── ProbeValueHistogramPlot.java │ └── ReadLengthHistogramPlot.java ├── LineGraph │ ├── LineGraphDialog.java │ └── LineGraphPanel.java ├── MAPlot │ ├── MAPlotDialog.java │ └── MAPlotPanel.java ├── ManualGenomeBuilder │ ├── ManualGenome.java │ ├── ManualGenomeBuilderDialog.java │ ├── ManualGenomeBuilderPanel.java │ ├── ManualGenomeChromosome.java │ └── ManualPseudoGenome.java ├── MemoryMonitor │ └── MemoryMonitor.java ├── PCAPlot │ ├── PCADataCalculator.java │ ├── PCAHistogramPanel.java │ ├── PCAScatterPlotDialog.java │ ├── PCAScatterPlotPanel.java │ ├── PCASource.java │ ├── PCAVarianceDialog.java │ ├── VarianceLineGraphPanel.java │ └── pca_template.r ├── ProbeListAnnotationSelector │ ├── ProbeListAnnotation.java │ └── ProbeListAnnotationSelectorDialog.java ├── ProbeListReport │ ├── ProbeListReport.java │ └── ProbeListReportCreator.java ├── ProbeSelectionListener.java ├── ProbeTrendPlot │ ├── TrendOverProbeDialog.java │ ├── TrendOverProbePanel.java │ ├── TrendOverProbePreferences.java │ └── TrendOverProbePreferencesDialog.java ├── QQDistributionPlot │ ├── QQDistributionDialog.java │ └── QQDistributionPanel.java ├── QuantitationTrendPlot │ ├── AxisScalePanel.java │ ├── HeatmapPanel │ │ ├── QuantitationHeatmapPanel.java │ │ └── QuantitationHeatmapPanelGroup.java │ ├── NamePanel.java │ ├── QuantitationTrendData.java │ ├── QuantitationTrendHeatmapDialog.java │ ├── QuantitationTrendHeatmapPreferencesDialog.java │ ├── QuantitationTrendPlotDialog.java │ ├── QuantitationTrendPlotPanel.java │ ├── QuantitationTrendPlotPreferencesDialog.java │ └── QuantitationTrendPlotPreferencesPanel.java ├── RNASeqQCPlot │ ├── DataStoreNamePanel.java │ ├── PercentileStripChart.java │ ├── RNAQCCalcualtor.java │ ├── RNAQCPreferencesDialog.java │ ├── RNAQCResult.java │ ├── RNAQCResultsDialog.java │ └── SampleSelectionListener.java ├── Report │ ├── InteractionReport │ │ ├── InteractionReportOptions.java │ │ └── InteractionReportTableDialog.java │ ├── ReportOptions.java │ └── ReportTableDialog.java ├── ScatterPlot │ ├── ScatterPlotDialog.java │ └── ScatterPlotPanel.java ├── SmallDoubleCellRenderer.java ├── SmallRNAQCPlot │ ├── FeatureNamePanel.java │ ├── SmallRNAQCCalcualtor.java │ ├── SmallRNAQCPreferencesDialog.java │ ├── SmallRNAQCResult.java │ ├── SmallRNAResultPanel.java │ └── SmallRNAResultsDialog.java ├── StarWars │ ├── MultiStarWarsDialog.java │ ├── MultiStarWarsPanel.java │ └── StarWarsPanel.java ├── StatusPanel.java ├── StrandBias │ ├── StrandBiasPlotDialog.java │ └── StrandBiasPlotPanel.java ├── TsneDataStorePlot │ ├── TsneDataStoreResult.java │ ├── TsneOptionsDialog.java │ └── tsne_template.r ├── VariancePlot │ ├── VariancePlotDialog.java │ └── VariancePlotPanel.java ├── Vistory │ ├── BlankPanel.java │ ├── ScrollablePanel.java │ ├── VistoryBlockButtons.java │ ├── VistoryDialog.java │ └── VistoryToolbar.java ├── VolcanoPlot │ ├── VolcanoPlotDialog.java │ └── VolcanoPlotPanel.java └── WelcomePanel │ ├── InitialSetupPanel.java │ ├── SeqMonkInformationPanel.java │ ├── SeqMonkTitlePanel.java │ └── WelcomePanel.java ├── ErrorCatcher.java ├── Filters ├── BinomialFilterForRev.java ├── BoxWhiskerFilter.java ├── ChiSquareFilter.java ├── ChiSquareFilterForRev.java ├── ChiSquareFilterFrontBack.java ├── CollateListsFilter.java ├── CombineFilter.java ├── CorrelationCluster │ ├── CorrelationCluster.java │ └── CorrelationClusterFilter.java ├── CorrelationFilter.java ├── DESeqFilter │ ├── DESeqFilter.java │ └── deseq_template.r ├── DeduplicationFilter.java ├── DifferencesFilter.java ├── DistributionPositionFilter.java ├── DuplicateListFilter.java ├── EdgeRFilter │ ├── EdgeRFilter.java │ ├── EdgeRForRevFilter.java │ ├── edger_for_rev_template.r │ └── edger_template.r ├── FeatureFilter.java ├── FeatureNameFilter.java ├── GeneSetFilter │ ├── GeneSetDisplay.java │ ├── GeneSetIntensityDifferenceFilter.java │ ├── GeneSetScatterPlotPanel.java │ └── ZScoreScatterPlotPanel.java ├── IntensityDifferenceFilter.java ├── IntersectListsFilter.java ├── LimmaFilter │ ├── LimmaFilter.java │ └── limma_template.r ├── ListAnnotationValuesFilter.java ├── LogisticRegressionFilter │ ├── LogisticRegressionFilter.java │ ├── LogisticRegressionSplicingFilter.java │ └── logistic_regression_template.r ├── ManualCorrelation │ ├── CorrelationProfileGraph.java │ └── ManualCorrelationFilter.java ├── MonteCarloFilter.java ├── OptionsListener.java ├── PositionFilter.java ├── ProbeFilter.java ├── ProbeGroupGenerator │ ├── ConsecutiveProbeGenerator.java │ ├── FeatureProbeGroupGenerator.java │ ├── ProbeGroupGenerator.java │ └── ProbeWindowGenerator.java ├── ProbeLengthFilter.java ├── ProbeNameFilter.java ├── ProportionOfLibraryStatisticsFilter.java ├── RandomFilter.java ├── ReplicateSetStatsFilter.java ├── SegmentationFilter │ ├── ClusteredSegment.java │ ├── SegmentClusteringDialog.java │ ├── SegmentationFilter.java │ └── segmentation_template.r ├── ValuesFilter.java ├── Variance │ ├── VarianceIntensityDifferenceFilter.java │ └── VarianceValuesFilter.java ├── WindowedDifferencesFilter.java ├── WindowedReplicateStatsFilter.java └── WindowedValuesFilter.java ├── GeneSets ├── GeneSet.java ├── GeneSetCollection.java ├── GeneSetCollectionParser.java └── MappedGeneSet.java ├── Gradients ├── ColourGradient.java ├── ColourIndexSet.java ├── GradientFactory.java ├── GreyscaleColourGradient.java ├── HotColdColourGradient.java ├── InvertedGradient.java ├── MagentaGreenColourGradient.java ├── RGB.java ├── RedGreenColourGradient.java ├── RedWhiteBlueColourGradient.java ├── RedWhiteColourGradient.java └── WhiteCyanBlueRedColourGradient.java ├── Importer └── SeqMonkImporter.java ├── Menu ├── HiCSeqMonkToolbar.java ├── MainSeqMonkToolbar.java ├── SeqMonkMenu.java ├── SeqMonkToolbar.java └── ToolbarPanel.java ├── Network ├── DownloadableGenomes │ ├── DownloadableGenomeSet.java │ ├── DownloadableGenomeTreeModel.java │ ├── GenomeAssembly.java │ ├── GenomeAssemblySet.java │ └── GenomeSpecies.java ├── GenomeDownloader.java ├── GenomeUpgrader.java └── UpdateChecker.java ├── Pipelines ├── AntisenseTranscriptionPipeline.java ├── BisulphiteFeaturePipeline.java ├── CodonBiasPipeline.java ├── GeneTrapQuantitationPipeline.java ├── IntronRegressionPipeline.java ├── Options │ └── DefinePipelineOptions.java ├── Pipeline.java ├── SplicingEfficiencyPipeline.java ├── Transcription │ ├── ActiveTranscriptionPipeline.java │ ├── FeatureGroup.java │ ├── IntronFeatureGroup.java │ ├── RNASeqParametersModel.java │ └── RNASeqPipeline.java ├── TranscriptionTerminationPipeline.java └── WigglePipeline.java ├── Preferences ├── ColourScheme.java ├── DisplayPreferences.java ├── DisplayPreferencesListener.java ├── Editor │ ├── DisplayPreferencesEditorDialog.java │ ├── DisplayPreferencesEditorPanel.java │ ├── NamedValueObject.java │ └── PreferencesListCellRenderer.java └── SeqMonkPreferences.java ├── ProbeGenerators ├── ContigProbeGenerator.java ├── CurrentRegionProbeGenerator.java ├── DeduplicationProbeGenerator.java ├── DefineProbeOptions.java ├── EvenCoverageProbeGenerator.java ├── FeaturePercentileProbeGenerator.java ├── FeatureProbeGenerator.java ├── InterstitialProbeGenerator.java ├── MacsPeakCaller.java ├── MergeConsecutiveProbeGenerator.java ├── ProbeGenerator.java ├── ProbeGeneratorListener.java ├── ProbeGeneratorProgressDialog.java ├── ProbeGeneratorUtilities.java ├── ProbeListProbeGenerator.java ├── RandomProbeGenerator.java ├── ReadPositionProbeGenerator.java ├── RunningWindowProbeGenerator.java └── ShuffleListProbeGenerator.java ├── Quantitation ├── BasePairQuantitation.java ├── CoverageDepthQuantitation.java ├── CoverageQuantitation.java ├── DifferenceQuantitation.java ├── DistanceToFeatureQuantitation.java ├── DuplicationQuantitation.java ├── EnrichmentNormalisationQuantitation.java ├── EnrichmentQuantitation.java ├── ExactOverlapQuantitation.java ├── FixedValueQuantitation.java ├── FourCEnrichmentQuantitation.java ├── HiCCisTransQuantitation.java ├── HiCPCADomainQuantitation.java ├── HiCPrevNextQuantitation.java ├── HiCReadCountQuantitation.java ├── LinearRegressionNormalisationQuantitation.java ├── LogTransformQuantitation.java ├── ManualCorrectionQuantitation.java ├── MatchDistributionsQuantitation.java ├── Options │ └── DefineQuantitationOptions.java ├── PerProbeNormalisationQuantitation.java ├── PercentileNormalisationQuantitation.java ├── ProbeLengthQuantitation.java ├── Quantitation.java ├── RankQuantitation.java ├── ReadCountQuantitation.java ├── RelativeQuantitation.java ├── SizeFactorNormalisationQuantitation.java ├── SmoothingQuantitation.java ├── SmoothingSubtractionQuantitation.java ├── StrandBiasQuantitation.java ├── SubsetNormalisationQuantitation.java └── ZScoreQuantitation.java ├── R ├── RException.java ├── RProgressListener.java ├── RScriptRunner.java └── RVersionTest.java ├── Reports ├── AnnotatedProbeReport.java ├── ChromosomeViewReport.java ├── DataStoreSummaryReport.java ├── FeatureReport.java ├── Interaction │ ├── AnnotatedInteractionReport.java │ └── InteractionReport.java ├── ProbeGroupReport.java └── Report.java ├── Resources ├── DisplayPrefsIcons │ ├── Bars.png │ ├── Blocks.png │ ├── Cold - Hot.png │ ├── Combined Strands.png │ ├── Gradient Colours.png │ ├── Greyscale.png │ ├── High Density.png │ ├── Indexed Colours.png │ ├── Lines.png │ ├── Low Density.png │ ├── Magenta - Green.png │ ├── Medium Density.png │ ├── Points.png │ ├── Positive Only.png │ ├── Positive and Negative.png │ ├── Probes Only.png │ ├── Reads Only.png │ ├── Reads and Probes.png │ ├── Red - Green.png │ ├── Red - White.png │ └── Separated Strands.png ├── StatusIcons │ ├── error.png │ ├── error.svg │ ├── information.png │ ├── information.svg │ ├── tick.png │ ├── tick.svg │ ├── warning.png │ └── warning.svg ├── Toolbar │ ├── add_text.png │ ├── add_title.png │ ├── change_annotation.png │ ├── change_data.png │ ├── change_data_zoom.png │ ├── clear_vistory.png │ ├── combine_pack_reads.svg │ ├── display_prefs.png │ ├── export_to_web.png │ ├── export_to_web.svg │ ├── find_feature.png │ ├── hiC_genome_heatmap.png │ ├── hiC_probe_heatmap.png │ ├── jump_to_position.png │ ├── launch_vistory.png │ ├── launch_vistory.svg │ ├── load_project.png │ ├── make_4c_dataset.png │ ├── new_project.png │ ├── paste_image.png │ ├── paste_image.svg │ ├── project_status.png │ ├── save_project.png │ └── split_pack_reads.svg ├── annotation_set_icon.png ├── annotation_set_icon.svg ├── babraham_bioinf_logo.png ├── bi_logo.png ├── datagroup_icon.png ├── datagroup_icon.svg ├── dataset_icon.png ├── dataset_icon.svg ├── hic_dataset_icon.png ├── hic_dataset_icon.svg ├── monk.svg ├── monk100.png ├── monk_dmg_background.png ├── monk_dmg_background.svg ├── monk_icon.svg ├── monk_logo.png ├── monk_vistory.png ├── monk_vistory.svg ├── probelist_icon.png ├── probelist_icon.svg ├── replicate_set_icon.png ├── replicate_set_icon.svg ├── sad_monk.svg ├── sad_monk100.png └── seqmonk.icns ├── SeqMonkApplication.java ├── SeqMonkException.java ├── Utilities ├── AxisScale.java ├── 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