├── .github ├── CONTRIBUTING.md ├── ISSUE_TEMPLATE.md ├── PULL_REQUEST_TEMPLATE.md └── workflows │ ├── planemo.yml │ ├── pypi.yml │ └── test.yml ├── .gitignore ├── .planemo.sh ├── .readthedocs.yaml ├── CHANGES.txt ├── LICENSE.txt ├── MANIFEST.in ├── README.md ├── README.rst ├── deeptools ├── SES_scaleFactor.py ├── __init__.py ├── alignmentSieve.py ├── bamCompare.py ├── bamCoverage.py ├── bamHandler.py ├── bamPEFragmentSize.py ├── bigwigAverage.py ├── bigwigCompare.py ├── cm.py ├── computeGCBias.py ├── computeMatrix.py ├── computeMatrixOperations.py ├── correctGCBias.py ├── correlation.py ├── correlation_heatmap.py ├── countReadsPerBin.py ├── deeptools_list_tools.py ├── estimateReadFiltering.py ├── estimateScaleFactor.py ├── getFragmentAndReadSize.py ├── getRatio.py ├── getScaleFactor.py ├── getScorePerBigWigBin.py ├── heatmapper.py ├── heatmapper_utilities.py ├── mapReduce.py ├── misc.py ├── multiBamSummary.py ├── multiBigwigSummary.py ├── parserCommon.py ├── plotCorrelation.py ├── plotCoverage.py ├── plotEnrichment.py ├── plotFingerprint.py ├── plotHeatmap.py ├── plotPCA.py ├── plotProfile.py ├── sumCoveragePerBin.py ├── test │ ├── __init__.py │ ├── skiptest_heatmapper_images.py │ ├── test_bamCoverage_and_bamCompare.py │ ├── test_bigwigAverage.py │ ├── test_bigwigCompare_and_multiBigwigSummary.py │ ├── test_computeMatrixOperations.py │ ├── test_corrGC │ │ ├── R_gc │ │ ├── R_gc_paired.txt │ │ ├── extra_sampling.bed │ │ ├── filter_out.bed │ │ ├── frequencies_data.txt │ │ ├── mappability.bg │ │ ├── mappability.bw │ │ ├── paired.bam │ │ ├── paired.bam.bai │ │ ├── sequence.2bit │ │ ├── sequence.fa │ │ ├── sequence.fa.fai │ │ ├── sizes │ │ ├── test.bam │ │ ├── test.bam.bai │ │ ├── test.sam │ │ ├── test_paired.bam │ │ ├── test_paired.bam.bai │ │ └── test_paired.sam │ ├── test_countReadsPerBin.py │ ├── test_data │ │ ├── computeMatrixOperations.bed │ │ ├── computeMatrixOperations.mat.gz │ │ ├── make_test_data.sh │ │ ├── othergenes.txt.gz │ │ ├── somegenes.txt.gz │ │ ├── test.bed3 │ │ ├── test.gtf │ │ ├── test1.bam │ │ ├── test1.bam.bai │ │ ├── test1.bg │ │ ├── test1.bw.bw │ │ ├── test1.cram │ │ ├── test1.cram.crai │ │ ├── test1.fa │ │ ├── test1.fa.fai │ │ ├── test1.sam │ │ ├── test2.bam │ │ ├── test2.bam.bai │ │ ├── test2.bg │ │ ├── test2.cram │ │ ├── test2.cram.crai │ │ ├── test2.sam │ │ ├── testA.bam │ │ ├── testA.bam.bai │ │ ├── testA.bw │ │ ├── testA.cram │ │ ├── testA.cram.crai │ │ ├── testA.fa │ │ ├── testA.fa.fai │ │ ├── testA.sam │ │ ├── testA_offset-1.bw │ │ ├── testA_offset1.bw │ │ ├── testA_offset1_10.bw │ │ ├── testA_offset20_-4.bw │ │ ├── testA_skipNAs.bw │ │ ├── testB.bam │ │ ├── testB.bam.bai │ │ ├── testB.bw │ │ ├── testB.cram │ │ ├── testB.cram.crai │ │ ├── testB.fa │ │ ├── testB.fa.fai │ │ ├── testB.sam │ │ ├── testB_skipNAs.bw │ │ ├── test_filtering.bam │ │ ├── test_filtering.bam.bai │ │ ├── test_filtering.blacklist.bed │ │ ├── test_filtering.cram │ │ ├── test_filtering.cram.crai │ │ ├── test_filtering.fa │ │ ├── test_filtering.fa.fai │ │ ├── test_filtering2.bam │ │ ├── test_filtering2.bam.bai │ │ ├── test_filtering2.cram │ │ ├── test_filtering2.cram.crai │ │ ├── test_paired.bam │ │ ├── test_paired.bam.bai │ │ ├── test_paired.sam │ │ ├── test_paired2.bam │ │ ├── test_paired2.bam.bai │ │ ├── test_paired2.bw │ │ ├── test_paired2.cram │ │ ├── test_paired2.cram.crai │ │ ├── test_paired2.fa │ │ ├── test_paired2.fa.fai │ │ ├── test_paired2.sam │ │ ├── test_proper_pair_filtering.bam │ │ └── test_proper_pair_filtering.bam.bai │ ├── test_heatmapper.py │ ├── test_heatmapper │ │ ├── group1.bed │ │ ├── group2.bed │ │ ├── heatmap_master_interpolation_bilinear.png │ │ ├── heatmap_master_multi_color.png │ │ ├── heatmap_master_multi_colormap_no_box.png │ │ ├── heatmap_master_multi_pergroup.png │ │ ├── large_matrix.mat.gz │ │ ├── make_test_data.sh │ │ ├── master.mat │ │ ├── master.mat.gz │ │ ├── master.png │ │ ├── master.tab │ │ ├── master_TES.mat │ │ ├── master_center.mat │ │ ├── master_extend_beyond_chr_size.mat │ │ ├── master_gtf.mat │ │ ├── master_metagene.mat │ │ ├── master_multi.mat │ │ ├── master_multi.mat.gz │ │ ├── master_multibed.mat │ │ ├── master_nan_to_zero.mat │ │ ├── master_relabeled.png │ │ ├── master_scale_reg.mat │ │ ├── master_scale_reg.mat.gz │ │ ├── master_scale_reg.png │ │ ├── master_unscaled.mat │ │ ├── out.bed │ │ ├── profile_master.png │ │ ├── profile_master_heatmap.png │ │ ├── profile_master_multi.png │ │ ├── profile_master_multi_pergroup.png │ │ ├── profile_master_overlap_lines.png │ │ ├── test.bed │ │ ├── test.bg │ │ ├── test.bw │ │ ├── test.sizes │ │ ├── test2.bed │ │ ├── unscaled.bed │ │ └── unscaled.bigWig │ ├── test_multiBamSummary.py │ ├── test_plotCoverage.py │ ├── test_plotCoverage │ │ ├── make_test_files.sh │ │ ├── outRawCounts_default.tabular │ │ └── plotCoverage_default.png │ ├── test_readFiltering.py │ ├── test_tools.py │ └── test_writeBedGraph.py ├── utilities.py ├── writeBedGraph.py └── writeBedGraph_bam_and_bw.py ├── docs ├── Makefile ├── _static │ ├── welcome_bamPE_out.png │ ├── welcome_base.css │ ├── welcome_bwCorr_spearman_hm.png │ ├── welcome_bwCorr_spearman_sc.png │ ├── welcome_eLife_chrX_heatmap.png │ ├── welcome_eLife_chrX_profile-1.png │ ├── welcome_eLife_chrX_profile.png │ ├── welcome_eLife_chrX_scaleR_heatmap.png │ ├── welcome_owl.carousel.css │ ├── welcome_owl.carousel.min.js │ └── welcome_owl.carousel.theme.css ├── conf.py ├── content │ ├── about.rst │ ├── advanced_features.rst │ ├── api.rst │ ├── changelog.rst │ ├── example_api_tutorial.rst │ ├── example_gallery.rst │ ├── example_step_by_step.rst │ ├── example_usage.rst │ ├── feature │ │ ├── blacklist.rst │ │ ├── effectiveGenomeSize.rst │ │ ├── metagene.rst │ │ ├── plotFingerprint_QC_metrics.rst │ │ ├── plotly.rst │ │ ├── read_extension.rst │ │ ├── read_offsets.rst │ │ └── unscaled_regions.rst │ ├── help_faq.rst │ ├── help_faq_galaxy.rst │ ├── help_galaxy_dataup.rst │ ├── help_galaxy_deeptools.rst │ ├── help_galaxy_intro.rst │ ├── help_glossary.rst │ ├── installation.rst │ ├── list_of_tools.rst │ └── tools │ │ ├── alignmentSieve.rst │ │ ├── bamCompare.rst │ │ ├── bamCoverage.rst │ │ ├── bamPEFragmentSize.rst │ │ ├── bigwigAverage.rst │ │ ├── bigwigCompare.rst │ │ ├── computeGCBias.rst │ │ ├── computeMatrix.rst │ │ ├── computeMatrixOperations.rst │ │ ├── correctGCBias.rst │ │ ├── estimateReadFiltering.rst │ │ ├── multiBamSummary.rst │ │ ├── multiBigwigSummary.rst │ │ ├── plotCorrelation.rst │ │ ├── plotCoverage.rst │ │ ├── plotEnrichment.rst │ │ ├── plotFingerprint.rst │ │ ├── plotHeatmap.rst │ │ ├── plotPCA.rst │ │ └── plotProfile.rst ├── images │ ├── GC_bias_simulated_reads_2L.png │ ├── GalHow_bamCompare.png │ ├── GalHow_bamCoverage.png │ ├── GalHow_clustHM01.png │ ├── GalHow_clustHM02.png │ ├── GalHow_clustHM03.png │ ├── GalHow_computeGCbias.png │ ├── GalHow_correctGCbias.png │ ├── GalHow_multiBamSummary.png │ ├── GalHow_plotCorrelation.png │ ├── GalHow_plotFingerprint.png │ ├── GalHow_profiles_XvsA02.png │ ├── GalHow_wf01.png │ ├── GalHow_wf02.png │ ├── Gal_DataLib.png │ ├── Gal_DataUpload.png │ ├── Gal_FAQ_IGV.png │ ├── Gal_FAQ_IGV_dataset.png │ ├── Gal_FAQ_UCSC01.png │ ├── Gal_FAQ_UCSC_dataset.png │ ├── Gal_FAQ_clusterLabeling.png │ ├── Gal_FAQ_filteringDuplicates.png │ ├── Gal_FAQ_info.png │ ├── Gal_UCSC.png │ ├── Gal_biomart.png │ ├── Gal_copy.png │ ├── Gal_filezilla.png │ ├── Gal_filter.png │ ├── Gal_historyReload.png │ ├── Gal_join.png │ ├── Gal_peaksVsBigWigs.png │ ├── Gal_screenshot_dataSet.png │ ├── Gal_screenshot_dataSetStates.png │ ├── Gal_startsite.png │ ├── Gal_startsite_with_comments.png │ ├── Gal_statistics.png │ ├── Gal_textfiles.png │ ├── Gal_workflow.png │ ├── QC_GCplots_input.png │ ├── QC_GCregionexclusion_UCSCscreenshot.png │ ├── QC_bamCorrelate_RNAseq.png │ ├── QC_bamCorrelate_intro.png │ ├── QC_fingerprint.png │ ├── QC_plotCoverage.png │ ├── bamFP_galaxy.png │ ├── bigwiCorr_galaxy.png │ ├── computeGCBias_Galaxy.png │ ├── computeMatrix_modes.png │ ├── computeMatrix_overview.png │ ├── correctGCBias_Galaxy.png │ ├── feature-blacklist0.png │ ├── feature-blacklist1.png │ ├── feature-metagene0.png │ ├── feature-metagene1.png │ ├── feature-offset0.png │ ├── feature-unscaled0.png │ ├── flowChart_FileFormats.png │ ├── gallery │ │ ├── Whyte_TypicalEnhancers_ESC.bed │ │ ├── coverage_Ibrahim.png │ │ ├── coverage_Ibrahim_thumb.png │ │ ├── hm_Bulut.png │ │ ├── hm_Bulut_thumb.png │ │ ├── hm_CpG.png │ │ ├── hm_CpG_thumb.png │ │ ├── hm_DNase.png │ │ ├── hm_DNase_thumb.png │ │ ├── hm_GC.png │ │ ├── hm_GC_thumb.png │ │ ├── hm_TATA.png │ │ ├── hm_TATA_thumb.png │ │ ├── hm_TATApsem.png │ │ ├── hm_TATApsem_thumb.png │ │ ├── hm_histonesGomez.png │ │ └── hm_histonesGomez_thumb.png │ ├── glossary_ascii.png │ ├── glossary_cigar.png │ ├── glossary_overview.png │ ├── glossary_sam.png │ ├── logo_mpi-ie.jpg │ ├── norm_IGVsnapshot_indFiles.png │ ├── norm_bamCoverage.png │ ├── plotCorrelation_galaxy.png │ ├── plotCoverage_annotated.png │ ├── plotFingerprintQC1.png │ ├── plotFingerprintQC2.png │ ├── plot_coverage.png │ ├── start_collage.png │ ├── start_workflow.png │ └── test_plots │ │ ├── ExampleComputeGCBias.png │ │ ├── ExampleComputeMatrix1.png │ │ ├── ExampleComputeMatrix2.png │ │ ├── ExampleComputeMatrix3.png │ │ ├── ExampleCorrectGCBias.png │ │ ├── ExampleFragmentSize.png │ │ ├── ExampleHeatmap1.png │ │ ├── ExampleHeatmap2.png │ │ ├── ExampleHeatmap3.png │ │ ├── ExampleHeatmap4.png │ │ ├── ExamplePlotCoverage.png │ │ ├── ExampleProfile1.png │ │ ├── ExampleProfile2.png │ │ ├── ExampleProfile3.png │ │ ├── ExampleProfile4.png │ │ ├── PCA_readCounts.png │ │ ├── bamFP_chrX.png │ │ ├── fingerprints.png │ │ ├── fragmentSize.png │ │ ├── heatmap_SpearmanCorr_readCounts.png │ │ ├── histoneMarks_corr-heatmap.png │ │ ├── histoneMarks_corr-scatter.png │ │ ├── plotEnrichment.png │ │ ├── scatterplot_PearsonCorr_bigwigScores.png │ │ └── testData_PCAplot.png ├── index.rst ├── requirements.txt └── source │ ├── _templates │ └── layout.html │ ├── deeptools.rst │ └── modules.rst ├── galaxy ├── workflows │ ├── 1_BAM_file_TO_Heatmap_of_read_coverages.ga │ ├── 2_BAM_files_TO_clustered_Heatmap_of_read_coverages.ga │ ├── Add_chr_to_first_column_of_a_6_columns_BED_file.ga │ ├── Clustered_heatmap_of_signals_around_the_TSSs__1_bigWig_TO_heatmap.ga │ ├── Compute_and_correct_GC_bias.ga │ ├── Remove_chr_from_the_beginning_of_genomic_interval_files.ga │ ├── readme.rst │ └── repository_dependencies.xml └── wrapper │ ├── .shed.yml │ ├── alignmentSieve.xml │ ├── bamCompare.xml │ ├── bamCoverage.xml │ ├── bamPEFragmentSize.xml │ ├── bigwigAverage.xml │ ├── bigwigCompare.xml │ ├── computeGCBias.xml │ ├── computeMatrix.xml │ ├── computeMatrixOperations.xml │ ├── correctGCBias.xml │ ├── deepTools_macros.xml │ ├── estimateReadFiltering.xml │ ├── multiBamSummary.xml │ ├── multiBigwigSummary.xml │ ├── plotCorrelation.xml │ ├── plotCoverage.xml │ ├── plotEnrichment.xml │ ├── plotFingerprint.xml │ ├── plotHeatmap.xml │ ├── plotPCA.xml │ ├── plotProfiler.xml │ ├── static │ └── images │ │ ├── GC_bias_simulated_reads_2L.png │ │ ├── QC_GCplots_input.png │ │ ├── QC_fingerprint.png │ │ ├── QC_multiBamSummary_humanSamples.png │ │ ├── QC_plotCoverage.png │ │ ├── bamCompare_output.png │ │ ├── bamCoverage_output.png │ │ ├── bamFP_galaxy_output.png │ │ ├── bamPEFragmentSize_output.png │ │ ├── bigwigCompare_output.png │ │ ├── computeGCBias_output.png │ │ ├── computeMatrix_advancedOutput.png │ │ ├── computeMatrix_output.png │ │ ├── computeMatrix_overview.png │ │ ├── computeMatrix_selectRegions.png │ │ ├── computeMatrix_selectScores.png │ │ ├── multiBamSummary_output.png │ │ ├── multiBigwigSummary_output.png │ │ ├── norm_IGVsnapshot_indFiles.png │ │ ├── plotCorrelate_RNAseq.png │ │ ├── plotCorrelation_galaxy_bw_heatmap_output.png │ │ ├── plotCorrelation_output.png │ │ ├── plotCorrelation_scatterplot_PearsonCorr_bigwigScores.png │ │ ├── plotCoverage_annotated.png │ │ ├── plotCoverage_output.png │ │ ├── plotEnrichment_output.png │ │ ├── plotFingerprint_output.png │ │ ├── plotHeatmap_example.png │ │ ├── plotHeatmap_example02.png │ │ ├── plotPCA_annotated.png │ │ ├── plotProfiler_examples.png │ │ ├── visual_hm_DmelPolII.png │ │ └── visual_profiler_DmelPolII.png │ ├── test-data │ ├── alignmentSieve.bam │ ├── alignmentSieve.bed │ ├── alignmentSieve.txt │ ├── alignmentSieve2.bam │ ├── alignmentSieve3.bam │ ├── bamCompare_result1.bg │ ├── bamCompare_result2.bw │ ├── bamCoverage_result1.bw │ ├── bamCoverage_result2.bw │ ├── bamCoverage_result3.bg │ ├── bamCoverage_result4.bg │ ├── bamCoverage_result4.bw │ ├── bamCoverage_result5.bw │ ├── bamCoverage_result6.bw │ ├── bamPEFragmentSize_histogram_result1.png │ ├── bamPEFragmentSize_lengths1.txt │ ├── bamPEFragmentSize_result1.txt │ ├── bamPEFragmentSize_table1.txt │ ├── bigwigAverage2.bw │ ├── bigwigCompare_result1.bw │ ├── bigwigCompare_result2.bg │ ├── bowtie2 test1.bam │ ├── computeGCBias_result1.png │ ├── computeGCBias_result1.tabular │ ├── computeMatrix1.bed │ ├── computeMatrix2.bed │ ├── computeMatrix2.bw │ ├── computeMatrixOperations.txt │ ├── computeMatrixOperations_result2.mat.gz │ ├── computeMatrix_result1.gz │ ├── computeMatrix_result2.gz │ ├── computeMatrix_result3.gz │ ├── correctGCBias_result1.bam │ ├── estimateReadFiltering.txt │ ├── heatmapper_result1.png │ ├── heatmapper_result2.png │ ├── heatmapper_result2.tabular │ ├── multiBamSummary_regions.bed │ ├── multiBamSummary_result1.npz │ ├── multiBamSummary_result2.npz │ ├── multiBamSummary_result2b.npz │ ├── multiBigwigSummary_result1.npz │ ├── multiBigwigSummary_result1.png │ ├── multiBigwigSummary_result2.npz │ ├── multiBigwigSummary_result2.tabular │ ├── paired_chr2L.bam │ ├── paired_chr2L.cram │ ├── phiX.2bit │ ├── phiX.bam │ ├── phiX.bam.bai │ ├── phiX.fasta │ ├── plotCorrelation_result1.png │ ├── plotCorrelation_result1.tabular │ ├── plotCorrelation_result2.png │ ├── plotCoverage.metrics │ ├── plotCoverage_result1.png │ ├── plotCoverage_result1.tabular │ ├── plotEnrichment_output.png │ ├── plotEnrichment_output.txt │ ├── plotFingerprint_quality_metrics.tabular │ ├── plotFingerprint_result1.png │ ├── plotFingerprint_result2.png │ ├── plotFingerprint_result2.tabular │ ├── plotPCA_result1.png │ ├── plotPCA_result2.png │ ├── plotPCA_result2.tabular │ ├── profiler_result1.png │ ├── profiler_result2.png │ ├── profiler_result2.tabular │ ├── sequence.2bit │ ├── test.bw │ ├── test_compated.bw │ └── test_half.bw │ ├── tool-data │ ├── deepTools_seqs.loc.sample │ └── lastz_seqs.loc.sample │ └── tool_data_table_conf.xml.sample ├── gallery ├── Whyte_TypicalEnhancers_ESC.bed ├── coverage_Ibrahim.png ├── coverage_Ibrahim_thumb.png ├── hm_Bulut.png ├── hm_Bulut_thumb.png ├── hm_CpG.png ├── hm_CpG_thumb.png ├── hm_DNase.png ├── hm_DNase_thumb.png ├── hm_GC.png ├── hm_GC_thumb.png ├── hm_TATA.png ├── hm_TATA_thumb.png ├── hm_TATApsem.png ├── hm_TATApsem_thumb.png ├── hm_histonesGomez.png └── hm_histonesGomez_thumb.png ├── pyproject.toml └── scripts ├── 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