├── .gitignore ├── .hgignore ├── .hgrc ├── .travis.yml ├── CGATPipelines ├── Pipeline │ ├── Cluster.py │ ├── Control.py │ ├── Database.py │ ├── Execution.py │ ├── Files.py │ ├── Local.py │ ├── Parameters.py │ ├── Utils.py │ └── __init__.py ├── PipelineBamStats.py ├── PipelineEnrichment.py ├── PipelineEnrichmentGSEA.py ├── PipelineExome.py ├── PipelineExomeAncestry.py ├── PipelineGO.py ├── PipelineGSEnrichment.py ├── PipelineGeneInfo.py ├── PipelineGeneset.py ├── PipelineGtfsubset.py ├── PipelineIntervalAnnotation.py ├── PipelineIntervals.py ├── PipelineMapping.py ├── PipelineMappingQC.py ├── PipelineMotifs.py ├── PipelinePeakcalling.py ├── PipelinePreprocess.py ├── PipelineReadqc.py ├── PipelineRnaseq.py ├── PipelineScRnaseqQc.py ├── PipelineSplicing.py ├── PipelineTracks.py ├── PipelineUCSC.py ├── PipelineWindows.py ├── __init__.py ├── cgatflow.py ├── configuration │ ├── conf.py │ └── pipeline.ini ├── export │ └── pipeline.svg ├── pipeline_bamstats.py ├── pipeline_bamstats │ ├── conf.py │ └── pipeline.ini ├── pipeline_chiptools.py ├── pipeline_chiptools │ ├── conf.py │ ├── example_design.tsv │ └── pipeline.ini ├── pipeline_docs │ ├── __init__.py │ ├── pipeline_annotations │ │ ├── __init__.py │ │ ├── contents.rst │ │ ├── pipeline │ │ │ ├── Bed.rst │ │ │ ├── Config.rst │ │ │ ├── GFF.rst │ │ │ ├── GTF.rst │ │ │ ├── Genesets.rst │ │ │ ├── Intervals.rst │ │ │ └── Status.rst │ │ └── trackers │ │ │ ├── AnnotationReport.py │ │ │ ├── Status.py │ │ │ └── __init__.py │ ├── pipeline_bamstats │ │ ├── Jupyter_report │ │ │ ├── CGAT_FULL_BAM_STATS_REPORT.ipynb │ │ │ ├── CGAT_bamstats_report.ipynb │ │ │ ├── CGAT_context_stats_report.ipynb │ │ │ ├── CGAT_exon_validation_report.ipynb │ │ │ ├── CGAT_fragment_library_type_report.ipynb │ │ │ ├── CGAT_idx_stats_report.ipynb │ │ │ ├── CGAT_picardstats_report.ipynb │ │ │ ├── CGAT_transcript_profile_report.ipynb │ │ │ ├── cgat_logo.jpeg │ │ │ └── oxford.png │ │ └── R_report │ │ │ ├── Base_distribution.Rmd │ │ │ ├── Idxstats.Rmd │ │ │ ├── Insert_size_hist.Rmd │ │ │ ├── Quality_by_cycle.Rmd │ │ │ ├── Quality_distribution.Rmd │ │ │ ├── Report.Rproj │ │ │ ├── Transcript_profile.Rmd │ │ │ ├── _site.yml │ │ │ ├── bamstats.Rmd │ │ │ ├── context_stats.Rmd │ │ │ ├── exon_validation.Rmd │ │ │ ├── index.Rmd │ │ │ ├── mapq.Rmd │ │ │ ├── nh_tag.Rmd │ │ │ └── strandness.Rmd │ ├── pipeline_chiptools │ │ └── Jupyter_report │ │ │ ├── GC content.ipynb │ │ │ ├── nucleotideFreq.ipynb │ │ │ ├── tagAutocorrelation.ipynb │ │ │ └── tagCountDistribution_plot.ipynb │ ├── pipeline_cpg │ │ ├── Makefile │ │ ├── contents.rst │ │ ├── pipeline.rst │ │ ├── pipeline │ │ │ ├── IntervalsByAvgVal.rst │ │ │ ├── IntervalsByCDSOverlap.rst │ │ │ ├── IntervalsByFoldChange.rst │ │ │ ├── IntervalsByLength.rst │ │ │ ├── IntervalsByPeakVal.rst │ │ │ ├── Mapping.rst │ │ │ ├── Methods.rst │ │ │ ├── macs.rst │ │ │ ├── macs_annotations.rst │ │ │ ├── macs_cgi_intervals.rst │ │ │ ├── macs_interval_comparison.rst │ │ │ ├── macs_intervals.rst │ │ │ ├── macs_long_intervals.rst │ │ │ ├── macs_low_cpg_intervals.rst │ │ │ ├── macs_parameter_correlation.rst │ │ │ ├── macs_shared_intervals.rst │ │ │ ├── macs_tss_intervals.rst │ │ │ ├── macs_unique_intervals.rst │ │ │ ├── predicted_cgis.rst │ │ │ ├── sicer.rst │ │ │ └── zinba.rst │ │ ├── server.py │ │ └── trackers │ │ │ ├── Mapping.py │ │ │ ├── Mapping.pyc │ │ │ ├── cpgReport.py │ │ │ ├── cpgReport.pyc │ │ │ ├── macs.py │ │ │ ├── macs.pyc │ │ │ ├── macs_annotations.py │ │ │ ├── macs_annotations.pyc │ │ │ ├── macs_cgi_intervals.py │ │ │ ├── macs_cgi_intervals.pyc │ │ │ ├── macs_interval_comparison.py │ │ │ ├── macs_interval_comparison.pyc │ │ │ ├── macs_interval_lists.py │ │ │ ├── macs_interval_lists.pyc │ │ │ ├── macs_intervals.py │ │ │ ├── macs_intervals.pyc │ │ │ ├── macs_parameter_correlation.py │ │ │ ├── macs_parameter_correlation.pyc │ │ │ ├── macs_shared_intervals.py │ │ │ ├── macs_shared_intervals.pyc │ │ │ ├── macs_tss_intervals.py │ │ │ ├── macs_tss_intervals.pyc │ │ │ ├── macs_unique_intervals.py │ │ │ ├── macs_unique_intervals.pyc │ │ │ ├── predicted_cgis.py │ │ │ ├── predicted_cgis.pyc │ │ │ ├── sicer.py │ │ │ ├── sicer.pyc │ │ │ ├── zinba.py │ │ │ └── zinba.pyc │ ├── pipeline_exome │ │ ├── Makefile │ │ ├── contents.rst │ │ ├── pipeline.rst │ │ ├── pipeline │ │ │ ├── Coverage.rst │ │ │ ├── Filtered.rst │ │ │ ├── Filtered_rec.rst │ │ │ ├── InsertSize.rst │ │ │ ├── Mapping.rst │ │ │ └── Variants.rst │ │ ├── server.py │ │ └── trackers │ │ │ ├── Coverage.py │ │ │ ├── Filtered.py │ │ │ ├── InsertSize.py │ │ │ ├── Mapping.py │ │ │ ├── VarStats.py │ │ │ ├── exomeReport.py │ │ │ └── exomeReport.pyc │ ├── pipeline_exome_cancer │ │ ├── Makefile │ │ ├── contents.rst │ │ ├── pipeline.rst │ │ ├── pipeline │ │ │ ├── Coverage.rst │ │ │ ├── Filtered.rst │ │ │ ├── Filtered_rec.rst │ │ │ ├── InsertSize.rst │ │ │ ├── Mapping.rst │ │ │ ├── Signature.rst │ │ │ └── Variants.rst │ │ ├── server.py │ │ └── trackers │ │ │ ├── Coverage.py │ │ │ ├── Filtered.py │ │ │ ├── InsertSize.py │ │ │ ├── Mapping.py │ │ │ ├── Signature.py │ │ │ ├── VarStats.py │ │ │ └── exomeReport.py │ ├── pipeline_intervals │ │ ├── __init__.py │ │ ├── contents.rst │ │ ├── pipeline │ │ │ ├── Annotations.rst │ │ │ ├── Binding.rst │ │ │ ├── Functions.rst │ │ │ ├── GeneModels.rst │ │ │ ├── GeneModelsFinalSummary.st │ │ │ ├── GenomicContext.rst │ │ │ ├── Intervals.rst │ │ │ ├── Mast.rst │ │ │ ├── Meme.rst │ │ │ ├── MemeGallery.rst │ │ │ ├── Nucleotide.rst │ │ │ ├── Overlap.rst │ │ │ ├── Peaks.rst │ │ │ ├── Profiles.rst │ │ │ ├── Running.rst │ │ │ ├── TSS.rst │ │ │ └── Tomtom.rst │ │ ├── trackers │ │ │ ├── Annotations.py │ │ │ ├── Binding.py │ │ │ ├── Context.py │ │ │ ├── Gat.py │ │ │ ├── GeneProfile.py │ │ │ ├── IntervalReport.py │ │ │ ├── IntervalReport.py.orig │ │ │ ├── Intervals.py │ │ │ ├── Motifs.py │ │ │ ├── Nucleotide.py │ │ │ ├── Overlaps.py │ │ │ ├── Peaks.py │ │ │ ├── TSS.py │ │ │ └── __init__.py │ │ └── usage.rst │ ├── pipeline_mapping │ │ ├── __init__.py │ │ ├── contents.rst │ │ ├── pipeline.rst │ │ ├── pipeline │ │ │ ├── Geneprofiles.rst │ │ │ ├── Mapping.rst │ │ │ ├── MappingAlignmentStatistics.rst │ │ │ ├── MappingComplexity.rst │ │ │ ├── MappingContext.rst │ │ │ ├── MappingRNA.rst │ │ │ ├── MappingStar.rst │ │ │ ├── MappingSummary.rst │ │ │ ├── MappingTophat.rst │ │ │ ├── Methods.rst │ │ │ ├── RNASeq.rst │ │ │ ├── ReferenceCoverage.rst │ │ │ ├── Status.rst │ │ │ └── Validation.rst │ │ └── trackers │ │ │ ├── Mapping.py │ │ │ ├── MappingReport.py │ │ │ ├── QC.py │ │ │ ├── Reference.py │ │ │ ├── Status.py │ │ │ ├── Validation.py │ │ │ └── __init__.py │ ├── pipeline_mapping_benchmark │ │ ├── Makefile │ │ ├── contents.rst │ │ ├── pipeline.rst │ │ ├── pipeline │ │ │ └── Mapping.rst │ │ ├── server.py │ │ └── trackers │ │ │ ├── Mapping.py │ │ │ ├── Mapping.pyc │ │ │ └── benchmarkReport.py │ ├── pipeline_metagenomeassembly │ │ ├── Makefile │ │ ├── analysis.rst │ │ ├── analysis │ │ │ ├── Discussion.rst │ │ │ ├── Introduction.rst │ │ │ ├── Methods.rst │ │ │ └── Results.rst │ │ ├── contents.rst │ │ ├── labbook │ │ │ ├── static │ │ │ │ └── labbook.css │ │ │ └── theme.conf │ │ ├── pipeline.rst │ │ ├── pipeline │ │ │ ├── AbundanceEstimation.rst │ │ │ ├── Assembly.rst │ │ │ ├── AssemblyCoverage.rst │ │ │ ├── FunctionalProfiling.rst │ │ │ ├── GeneFinding.rst │ │ │ ├── Introduction.rst │ │ │ ├── KnownSpecies.rst │ │ │ ├── PipelineTest.rst │ │ │ └── ReadSummary.rst │ │ ├── pipeline_metagenomeassembly.py │ │ ├── server.py │ │ ├── sphinxreport.ini │ │ ├── trackers │ │ │ ├── Assembly.py │ │ │ ├── AssemblyCoverage.py │ │ │ ├── FunctionalProfile.py │ │ │ ├── GeneFinding.py │ │ │ ├── ReadSummary.py │ │ │ ├── RelativeAbundance.py │ │ │ ├── Trackers.rst │ │ │ └── knownSpecies.py │ │ └── usage.rst │ ├── pipeline_metagenomebenchmark │ │ ├── Makefile │ │ ├── analysis.rst │ │ ├── analysis │ │ │ ├── Discussion.rst │ │ │ ├── Introduction.rst │ │ │ ├── Methods.rst │ │ │ └── Results.rst │ │ ├── contents.rst │ │ ├── labbook │ │ │ ├── static │ │ │ │ └── labbook.css │ │ │ └── theme.conf │ │ ├── pipeline.rst │ │ ├── pipeline │ │ │ └── GenomeCoverage.rst │ │ ├── pipeline_metagenomebenchmark.py │ │ ├── sphinxreport.ini │ │ └── trackers │ │ │ └── GenomeCoverage.py │ ├── pipeline_metagenomecommunities │ │ ├── Makefile │ │ ├── contents.rst │ │ ├── labbook │ │ │ ├── static │ │ │ │ └── labbook.css │ │ │ └── theme.conf │ │ ├── pipeline.rst │ │ ├── pipeline │ │ │ ├── Assembly.rst │ │ │ ├── AssemblyCoverage.rst │ │ │ ├── FunctionalProfiling.rst │ │ │ ├── Introduction.rst │ │ │ ├── LcaAbundance.rst │ │ │ ├── MetaphlanAbundance.rst │ │ │ ├── PipelineTest.rst │ │ │ └── ReadSummary.rst │ │ ├── server.py │ │ ├── sphinxreport.ini │ │ ├── trackers │ │ │ ├── ReadSummary.py │ │ │ └── Trackers.rst │ │ └── usage.rst │ ├── pipeline_motifs │ │ ├── __init__.py │ │ ├── analysis.rst │ │ ├── contents.rst │ │ ├── pipeline.rst │ │ ├── pipeline │ │ │ ├── GeneModels.rst │ │ │ ├── GeneModelsFinalSummary.st │ │ │ ├── Mast.rst │ │ │ ├── Meme.rst │ │ │ ├── MemeChip.rst │ │ │ ├── MemeGallery.rst │ │ │ ├── Running.rst │ │ │ └── Tomtom.rst │ │ ├── trackers │ │ │ ├── Annotations.py │ │ │ ├── Binding.py │ │ │ ├── Context.py │ │ │ ├── Gat.py │ │ │ ├── GeneProfile.py │ │ │ ├── IntervalReport.py │ │ │ ├── Intervals.py │ │ │ ├── Motifs.py │ │ │ ├── Nucleotide.py │ │ │ ├── Peaks.py │ │ │ ├── TSS.py │ │ │ └── __init__.py │ │ └── usage.rst │ ├── pipeline_peakcalling │ │ ├── __init__.py │ │ ├── contents.rst │ │ ├── notebooks │ │ │ ├── template_peakcalling_filtering_Report.ipynb │ │ │ ├── template_peakcalling_filtering_Report_insert_sizes.ipynb │ │ │ ├── template_peakcalling_filtering_Report_reads_per_chr.ipynb │ │ │ ├── template_peakcalling_peakstats.ipynb │ │ │ └── template_peakcalling_report_contents.ipynb │ │ ├── pipeline │ │ │ ├── Annotations.rst │ │ │ ├── Binding.rst │ │ │ ├── Callers.rst │ │ │ ├── Correlations.rst │ │ │ ├── Encode.rst │ │ │ ├── Export.rst │ │ │ ├── IDR.rst │ │ │ ├── IntervalLists.rst │ │ │ ├── IntervalsPeaks.rst │ │ │ ├── IntervalsRegions.rst │ │ │ ├── IntervalsSummits.rst │ │ │ ├── MACS.rst │ │ │ ├── MACS2.rst │ │ │ ├── Mapping.rst │ │ │ ├── Methods.rst │ │ │ ├── Overlaps.rst │ │ │ ├── Peaks.rst │ │ │ ├── Reproducibility.rst │ │ │ ├── SICER.rst │ │ │ ├── SPP.rst │ │ │ ├── Status.rst │ │ │ └── TSS.rst │ │ ├── trackers │ │ │ ├── Annotations.py │ │ │ ├── Distances.py │ │ │ ├── Intervals.py │ │ │ ├── Mapping.py │ │ │ ├── Overlaps.py │ │ │ ├── PeakCalling.py │ │ │ ├── PeakcallingReport.py │ │ │ ├── ReadsUnderPeaks.py │ │ │ ├── Status.py │ │ │ ├── TSS.py │ │ │ └── Tracks.py │ │ └── usage.rst │ ├── pipeline_proj007 │ │ ├── Makefile │ │ ├── contents.rst │ │ ├── pipeline.rst │ │ ├── pipeline │ │ │ ├── .peakshape.rst.swp │ │ │ ├── Mapping.rst │ │ │ ├── Methods.rst │ │ │ ├── genome_composition.rst │ │ │ ├── macs.rst │ │ │ ├── macs_replicated_genes_with_nmi.rst │ │ │ ├── macs_replicated_interval_associations.rst │ │ │ ├── macs_replicated_interval_comparison.rst │ │ │ ├── macs_replicated_interval_genomic_features.rst │ │ │ ├── macs_replicated_interval_noncoding.rst │ │ │ ├── macs_replicated_interval_peakshape.rst │ │ │ ├── macs_replicated_interval_tss_distance.rst │ │ │ ├── macs_replicated_intervals.rst │ │ │ ├── macs_replicated_intervals_per_contig.rst │ │ │ ├── macs_replicated_long_interval_capseq_profile.rst │ │ │ ├── macs_replicated_long_interval_chromatin_profile.rst │ │ │ ├── macs_replicated_long_interval_go_analysis.rst │ │ │ ├── macs_replicated_long_interval_polycomb.rst │ │ │ ├── macs_replicated_long_interval_tissue_conservation.rst │ │ │ ├── macs_replicated_long_intervals.rst │ │ │ ├── macs_replicated_overlapped_genes.rst │ │ │ ├── macs_replicated_overlapped_genes_capseq_profile.rst │ │ │ ├── macs_replicated_overlapped_genes_chromatin_profile.rst │ │ │ ├── macs_replicated_overlapped_genes_control.rst │ │ │ ├── macs_replicated_overlapped_genes_go_analysis.rst │ │ │ ├── macs_replicated_overlapped_genes_polycomb.rst │ │ │ ├── macs_replicated_overlapped_genes_tissue_conservation.rst │ │ │ ├── macs_replicated_shared_intervals.rst │ │ │ ├── macs_replicated_tissue_specific_intervals.rst │ │ │ ├── macs_replicated_tss_intervals.rst │ │ │ ├── macs_replicated_unique_interval_chromatin_profile.rst │ │ │ ├── macs_replicated_unique_intervals.rst │ │ │ └── predicted_cgis.rst │ │ ├── server.py │ │ └── trackers │ │ │ ├── .macs_cgi_intervals.py.swp │ │ │ ├── .macs_replicated_interval_tss_distance.py.swp │ │ │ ├── .macs_replicated_intervals_noncoding.py.swp │ │ │ ├── Mapping.py │ │ │ ├── cpgReport.py │ │ │ ├── genome_composition.py │ │ │ ├── macs.py │ │ │ ├── macs_annotations.py │ │ │ ├── macs_cgi_intervals.py │ │ │ ├── macs_genomic_features.py │ │ │ ├── macs_genomic_locations.py │ │ │ ├── macs_interval_comparison.py │ │ │ ├── macs_interval_lists.py │ │ │ ├── macs_intervals.py │ │ │ ├── macs_parameter_correlation.py │ │ │ ├── macs_replicated_genes_with_nmi.py │ │ │ ├── macs_replicated_interval_annotations.py │ │ │ ├── macs_replicated_interval_associations.py │ │ │ ├── macs_replicated_interval_comparison.py │ │ │ ├── macs_replicated_interval_genomic_features.py │ │ │ ├── macs_replicated_interval_noncoding.py │ │ │ ├── macs_replicated_interval_rnaseq_tss.py │ │ │ ├── macs_replicated_interval_tss_distance.py │ │ │ ├── macs_replicated_intervals.py │ │ │ ├── macs_replicated_intervals_per_contig.py │ │ │ ├── macs_replicated_liver_testes_shared_intervals.py │ │ │ ├── macs_replicated_liver_testes_unique_intervals.py │ │ │ ├── macs_replicated_long_interval_capseq_profile.py │ │ │ ├── macs_replicated_long_interval_chromatin_profile.py │ │ │ ├── macs_replicated_long_interval_genes.py │ │ │ ├── macs_replicated_overlapped_genes.py │ │ │ ├── macs_replicated_shared_intervals.py │ │ │ ├── macs_replicated_tissue_specific_intervals.py │ │ │ ├── macs_replicated_unique_interval_chromatin_profile.py │ │ │ ├── macs_replicated_unique_intervals.py │ │ │ ├── macs_shared_intervals.py │ │ │ ├── macs_tss_intervals.py │ │ │ ├── macs_unique_intervals.py │ │ │ ├── peakshape.py │ │ │ └── predicted_cgis.py │ ├── pipeline_readqc │ │ ├── __init__.py │ │ ├── contents.rst │ │ ├── pipeline.rst │ │ ├── pipeline │ │ │ ├── AdapterContent.rst │ │ │ ├── BaseQuality.rst │ │ │ ├── ExperimentQuality.rst │ │ │ ├── FastQC.rst │ │ │ ├── FastqScreen.rst │ │ │ ├── Filtering.rst │ │ │ ├── GeneModelsFinalSummary.st │ │ │ ├── KmerProfiles.rst │ │ │ ├── OverRepresentedSequences.rst │ │ │ ├── PerBaseNContent.rst │ │ │ ├── PerSequenceGCContent.rst │ │ │ ├── PerSequenceQuality.rst │ │ │ ├── SequenceDuplicationLevels.rst │ │ │ ├── SequenceLength.rst │ │ │ ├── SideBySide.rst │ │ │ └── Summary.rst │ │ └── trackers │ │ │ ├── ReadQuality.py │ │ │ ├── ReadqcReport.py │ │ │ ├── Status.py │ │ │ └── __init__.py │ ├── pipeline_rnaseqdiffexpression │ │ ├── contents.rst │ │ ├── pipeline.rst │ │ ├── pipeline │ │ │ ├── DESeqDiagnostics.rst │ │ │ ├── DEseq_result.rst │ │ │ ├── EdgeRDiagnostics.rst │ │ │ ├── EdgeR_result.rst │ │ │ ├── ExpressionTables.rst │ │ │ ├── SleuthDiagnostics.rst │ │ │ ├── Sleuth_result.rst │ │ │ └── Summary.rst │ │ └── trackers │ │ │ ├── Expression.py │ │ │ ├── Genelists.py │ │ │ ├── Isoform.py │ │ │ ├── IsoformReport.py │ │ │ ├── Results.py │ │ │ ├── Status.py │ │ │ └── __init__.py │ ├── pipeline_rnaseqlncrna │ │ ├── Makefile │ │ ├── analysis.rst │ │ ├── analysis │ │ │ ├── Discussion.rst │ │ │ ├── Introduction.rst │ │ │ ├── Methods.rst │ │ │ └── Results.rst │ │ ├── contents.rst │ │ ├── labbook │ │ │ ├── static │ │ │ │ └── labbook.css │ │ │ └── theme.conf │ │ ├── pipeline.rst │ │ ├── pipeline │ │ │ ├── Classification.rst │ │ │ ├── Cpc.rst │ │ │ ├── LncRNACount.rst │ │ │ └── Summary.rst │ │ ├── server.py │ │ ├── trackers │ │ │ ├── CPC.py │ │ │ ├── Classification.py │ │ │ ├── LncRNACounts.py │ │ │ ├── Summary.py │ │ │ ├── Trackers.py │ │ │ └── Trackers.rst │ │ └── usage.rst │ ├── pipeline_rnaseqqc │ │ ├── __init__.py │ │ ├── contents.rst │ │ ├── contents.rst-ToAIMFor │ │ ├── pipeline │ │ │ ├── ExpressionDistribution.rst │ │ │ ├── bias.rst │ │ │ ├── bias.rstTOAIMFOR │ │ │ ├── bias │ │ │ │ ├── chromosomebias.rst │ │ │ │ ├── endbias.rst │ │ │ │ ├── lanebias.rst │ │ │ │ ├── sequence_context_bias.rst │ │ │ │ └── strandbias.rst │ │ │ ├── clustering.rst │ │ │ ├── clustering │ │ │ │ ├── MDS.rst │ │ │ │ ├── PCA.rst │ │ │ │ ├── heatmap.rst │ │ │ │ └── sample_overlaps.rst │ │ │ ├── context.rst │ │ │ ├── context.rstTOAIMFOR │ │ │ ├── context │ │ │ │ ├── contextproportion.rst │ │ │ │ └── transcriptomeproportion.rst │ │ │ ├── design.rst │ │ │ ├── endbias.rst │ │ │ ├── functionalenrichment.rst │ │ │ ├── genes.rst │ │ │ ├── genesofinterest.py │ │ │ ├── genesofinterest.rst │ │ │ ├── methods.rst │ │ │ ├── overview.rst │ │ │ ├── pipeline_summary.rst │ │ │ ├── saturation.rst │ │ │ ├── strandedness.rst │ │ │ ├── template.rst │ │ │ ├── topexpressed.rst │ │ │ ├── validation.rst │ │ │ └── validation │ │ │ │ ├── functionalenrichment.rst │ │ │ │ ├── genes.rst │ │ │ │ └── topexpressed.rst │ │ └── trackers │ │ │ ├── RnaseqqcReport.py │ │ │ └── __init__.py │ ├── pipeline_rnaseqtranscripts │ │ ├── __init__.py │ │ ├── analysis.rst │ │ ├── contents.rst │ │ ├── pipeline.rst │ │ ├── pipeline │ │ │ ├── Export.rst │ │ │ ├── GeneModels.rst │ │ │ ├── GeneModelsBenchmark.rst │ │ │ ├── GeneModelsFinalSummary.rst │ │ │ ├── GeneModelsFinalSummary.st │ │ │ ├── GeneModelsGeneSet.rst │ │ │ ├── GeneModelsReproducibility.rst │ │ │ ├── GeneModelsSummary.rst │ │ │ ├── GeneModelsTranscripts.rst │ │ │ ├── Methods.rst │ │ │ ├── ReferenceCoverage.rst │ │ │ ├── Status.rst │ │ │ └── TranscriptModelling.rst │ │ ├── trackers │ │ │ ├── Expression.py │ │ │ ├── Genemodels.py │ │ │ ├── Lincrna.py │ │ │ ├── QC.py │ │ │ ├── Reference.py │ │ │ ├── RnaseqTranscriptsReport.py │ │ │ ├── Status.py │ │ │ ├── Validation.py │ │ │ └── __init__.py │ │ └── usage.rst │ ├── pipeline_rrbs │ │ ├── Makefile │ │ ├── contents.rst │ │ ├── exploratory │ │ │ └── heatmaps.rst │ │ ├── exploratoryDataAnalysis.rst │ │ ├── qc.rst │ │ ├── qc │ │ │ ├── coverage.rst │ │ │ ├── methylationBySample.rst │ │ │ ├── readPositionsMethylationBias.rst │ │ │ └── threeprime.rst │ │ ├── regions.rst │ │ ├── regions │ │ │ └── regionsM3D.rst │ │ ├── server.py │ │ ├── tables.rst │ │ └── trackers │ │ │ ├── Coverage.py │ │ │ ├── M3D.py │ │ │ └── rrbsReport.py │ ├── pipeline_scrnaseqqc │ │ ├── __init__.py │ │ ├── _templates │ │ │ └── cgat_logo.png │ │ ├── contents.rst │ │ ├── pipeline.rst │ │ ├── pipeline │ │ │ ├── Dummy.rst │ │ │ └── Methods.rst │ │ └── trackers │ │ │ └── TemplateReport.py │ ├── pipeline_species_conservation │ │ ├── Makefile │ │ ├── contents.rst │ │ ├── pipeline.rst │ │ ├── pipeline │ │ │ ├── conserved_genes.rst │ │ │ ├── orthology_stats.rst │ │ │ └── pairwise_orthologs.rst │ │ ├── server.py │ │ └── trackers │ │ │ ├── orthology.py │ │ │ └── orthology.pyc │ ├── pipeline_splicing │ │ ├── __init__.py │ │ ├── _templates │ │ │ └── cgat_logo.png │ │ ├── contents.rst │ │ ├── pipeline.rst │ │ ├── pipeline │ │ │ ├── Dummy.rst │ │ │ └── Methods.rst │ │ └── trackers │ │ │ └── TemplateReport.py │ ├── pipeline_template │ │ ├── __init__.py │ │ ├── analysis.rst │ │ ├── contents.rst │ │ ├── pipeline.rst │ │ ├── pipeline │ │ │ ├── GeneModelsFinalSummary.st │ │ │ └── Running.rst │ │ ├── trackers │ │ │ ├── TemplateReport.py │ │ │ └── __init__.py │ │ └── usage.rst │ ├── pipeline_testing │ │ ├── __init__.py │ │ ├── contents.rst │ │ ├── pipeline │ │ │ ├── Config.rst │ │ │ ├── Details.rst │ │ │ ├── Methods.rst │ │ │ └── Status.rst │ │ └── trackers │ │ │ ├── Status.py │ │ │ ├── TestingReport.py │ │ │ └── __init__.py │ ├── pipeline_windows │ │ ├── Makefile │ │ ├── contents.rst │ │ ├── pipeline │ │ │ ├── Config.rst │ │ │ ├── CpGCoverage.rst │ │ │ ├── DESeq.rst │ │ │ ├── DESeqDMR.rst │ │ │ ├── DESeqDispersion.rst │ │ │ ├── DESeqFDR.rst │ │ │ ├── DESeqHeatmaps.rst │ │ │ ├── DESeqMAPlots.rst │ │ │ ├── DESeqPvalue.rst │ │ │ ├── DESeqSizeFactors.rst │ │ │ ├── DESeqSpike.rst │ │ │ ├── DifferentialMethylation.rst │ │ │ ├── EdgeR.rst │ │ │ ├── EdgeRDMR.rst │ │ │ ├── EdgeRMAPlots.rst │ │ │ ├── EdgeRSpike.rst │ │ │ ├── Export.rst │ │ │ ├── GenomicContext.rst │ │ │ ├── HilbertCurves.rst │ │ │ ├── Medips.rst │ │ │ ├── MedipsQCPlots.rst │ │ │ ├── MedipsResults.rst │ │ │ ├── Processing.rst │ │ │ ├── Profiles.rst │ │ │ └── Signal.rst │ │ ├── server.py │ │ └── trackers │ │ │ ├── CpGCoverage.py │ │ │ ├── DifferentialMethylation.py │ │ │ ├── GenomicContext.py │ │ │ ├── ImageTracker.py │ │ │ ├── MedipReport.py │ │ │ ├── Profiles.py │ │ │ ├── Signal.py │ │ │ ├── Status.py │ │ │ └── Tiling.py │ ├── sphinxreport.log │ └── themes │ │ ├── cgat │ │ ├── layout.html │ │ ├── static │ │ │ ├── cgat.css_t │ │ │ ├── jquery.dataTables.min.js │ │ │ ├── jquery.min.js │ │ │ ├── jssor.js │ │ │ ├── jssor.slider.js │ │ │ ├── notebook.js │ │ │ └── sorttable.js │ │ └── theme.conf │ │ └── cgat_logo.png ├── pipeline_enrichment.py ├── pipeline_enrichment │ ├── conf.py │ └── pipeline.ini ├── pipeline_exome.py ├── pipeline_exome │ ├── pipeline.ini │ └── sphinxreport.ini ├── pipeline_exome_cancer.py ├── pipeline_exome_cancer │ ├── pipeline.ini │ └── sphinxreport.ini ├── pipeline_geneinfo.py ├── pipeline_geneinfo │ ├── conf.py │ └── pipeline.ini ├── pipeline_genesets.py ├── pipeline_genesets │ ├── conf.py │ └── pipeline.ini ├── pipeline_gwas.py ├── pipeline_gwas │ ├── conf.py │ └── pipeline.ini ├── pipeline_intervals.py ├── pipeline_intervals │ ├── pipeline.ini │ └── sphinxreport.ini ├── pipeline_mapping.py ├── pipeline_mapping │ ├── pipeline.ini │ └── sphinxreport.ini ├── pipeline_motifs.py ├── pipeline_motifs │ ├── pipeline.ini │ └── sphinxreport.ini ├── pipeline_peakcalling.py ├── pipeline_peakcalling │ ├── conf.py │ ├── example_design.tsv │ └── pipeline.ini ├── pipeline_quickstart.py ├── pipeline_quickstart │ └── sphinxreport.ini ├── pipeline_readqc.py ├── pipeline_readqc │ ├── pipeline.ini │ └── sphinxreport.ini ├── pipeline_rnaseq │ ├── pipeline.ini │ └── sphinxreport.ini ├── pipeline_rnaseqdiffexpression.py ├── pipeline_rnaseqdiffexpression │ ├── pipeline.ini │ └── sphinxreport.ini ├── pipeline_rnaseqqc.py ├── pipeline_rnaseqqc │ ├── pipeline.ini │ └── sphinxreport.ini ├── pipeline_ruffus_example.py ├── pipeline_scrnaseqqc.py ├── pipeline_scrnaseqqc │ ├── conf.py │ └── pipeline.ini ├── pipeline_splicing.py ├── pipeline_splicing │ ├── conf.py │ └── pipeline.ini ├── pipeline_template.py ├── pipeline_template │ └── pipeline.ini ├── pipeline_template_data │ ├── Dummy.rst │ ├── Methods.rst │ ├── TemplateReport.py │ ├── __init__.py │ ├── cgat_logo.png │ ├── conf.py │ ├── contents.rst │ ├── pipeline.ini │ ├── pipeline.rst │ ├── pipeline_template_full.py │ ├── pipeline_template_minimal.py │ ├── sphinxreport.ini │ └── themes │ │ └── cgat │ │ ├── layout.html │ │ ├── static │ │ ├── cgat.css_t │ │ └── sorttable.js │ │ └── theme.conf ├── pipeline_testing.py ├── pipeline_testing │ ├── pipeline.ini │ └── sphinxreport.ini ├── pipeline_windows.py └── pipeline_windows │ ├── pipeline.ini │ └── sphinxreport.ini ├── INSTALL ├── KNOWN_BUGS ├── LICENSE ├── MANIFEST.in ├── PKG-INFO ├── R ├── DESeq_utils.R ├── multiplot.R ├── run_spp.R ├── run_zinba.R ├── venn_diagram.R └── wiggle2hilbert.R ├── README.rst ├── THANKS.txt ├── conda └── environments │ ├── pipeline-bamstats-template.yml │ ├── pipeline-chiptools-template.yml │ ├── pipeline-enrichment-template.yml │ ├── pipeline-genesets-template.yml │ ├── pipeline-intervals-template.yml │ ├── pipeline-mapping-template.yml │ ├── pipeline-peakcalling-sicer.yml │ ├── pipeline-peakcalling-template.yml │ ├── pipeline-readqc-template.yml │ ├── pipeline-rnaseqde-template.yml │ ├── pipeline-rnaseqqc-template.yml │ ├── pipeline-scrnaseqqc-template.yml │ ├── pipeline-windows-template.yml │ ├── pipelines-devel-template.yml │ ├── pipelines-devel.yml │ ├── pipelines-extra-template.yml │ ├── pipelines-extra.yml │ ├── pipelines-ide.yml │ ├── pipelines-nosetests-template.yml │ ├── pipelines-nosetests.yml │ ├── pipelines-production-template.yml │ ├── pipelines-production.yml │ └── pipelines-py2.yml ├── doc ├── BuildingPipelines.rst ├── CGATPipelines.rst ├── Developers.rst ├── InstallingPipelines.rst ├── Makefile ├── PipelineReports.rst ├── PipelinesBackground.rst ├── Reference.rst ├── Release.rst ├── Tutorials.rst ├── UsingPipelines.rst ├── _templates │ └── cgat_logo.png ├── collect.py ├── conf.py ├── glossary.rst ├── images │ ├── Figure_for_documentation.png │ └── Figure_pipelines.png ├── index.rst ├── modules.rst ├── pipelinemodules │ ├── Pipeline.rst │ ├── Pipeline │ │ ├── Control.rst │ │ ├── Database.rst │ │ ├── Execution.rst │ │ ├── Files.rst │ │ ├── Local.rst │ │ └── Utils.rst │ ├── PipelineDatabase.rst │ ├── PipelineEnrichment.rst │ ├── PipelineExome.rst │ ├── PipelineGO.rst │ ├── PipelineGeneset.rst │ ├── PipelineIntervalAnnotation.rst │ ├── PipelineKEGG.rst │ ├── PipelineLncRNA.rst │ ├── PipelineMapping.rst │ ├── PipelineMappingQC.rst │ ├── PipelineMetagenomeBenchmark.rst │ ├── PipelineMetagenomeCommunities.rst │ ├── PipelineMotifs.rst │ ├── PipelinePeakcalling.rst │ ├── PipelinePreprocess.rst │ ├── PipelineReadqc.rst │ ├── PipelineRnaseq.rst │ ├── PipelineRrbs.rst │ ├── PipelineTimeseries.rst │ ├── PipelineTracks.rst │ ├── PipelineTransfacMatch.rst │ ├── PipelineUCSC.rst │ └── PipelineWindows.rst ├── pipelines │ ├── pipeline_annotations.rst │ ├── pipeline_exome.rst │ ├── pipeline_exome_cancer.rst │ ├── pipeline_expression.rst │ ├── pipeline_fastqToBigWig.rst │ ├── pipeline_intervals.rst │ ├── pipeline_mapping.rst │ ├── pipeline_mapping_benchmark.rst │ ├── pipeline_metagenomecommunities.rst │ ├── pipeline_motifs.rst │ ├── pipeline_peakcalling.rst │ ├── pipeline_readqc.rst │ ├── pipeline_rnaseq.rst │ ├── pipeline_rnaseqdiffexpression.rst │ ├── pipeline_rnaseqlncrna.rst │ ├── pipeline_rnaseqqc.rst │ ├── pipeline_rnaseqtranscripts.rst │ ├── pipeline_rrbs.rst │ ├── pipeline_template.rst │ ├── pipeline_testing.rst │ ├── pipeline_timeseries.rst │ ├── pipeline_transfacmatch.rst │ └── pipeline_windows.rst ├── plots │ ├── H3K4me1_heatmap.png │ ├── H3K4me3_heatmap.png │ ├── metagenome_contigs_tetra.png │ ├── nfkb_profile.pdf │ └── nfkb_profile.png ├── python │ └── Trackers.py ├── scripts.rst ├── scripts │ ├── cgat_build_report_page.rst │ ├── cgat_clean.rst │ ├── cgat_cluster_distribute.rst │ ├── cgat_cwd2list.rst │ ├── cgat_logfiles2tsv.rst │ ├── cgat_ruffus_profile.rst │ ├── cgat_tsv2links.rst │ ├── cgat_zap.rst │ ├── farm.rst │ ├── nofarm.rst │ ├── pipeline_quickstart.rst │ ├── qkill.rst │ ├── run.rst │ ├── run_function.rst │ ├── submit.rst │ └── version.rst └── styleguide.rst ├── external_dependencies.txt ├── install-CGAT-tools.sh ├── obsolete ├── PipelineChipseq.py ├── PipelineGO.py ├── PipelineIDR.py ├── PipelineKEGG.py ├── PipelineLncRNA.py ├── PipelineMedip.py ├── PipelineMetagenomeBenchmark.py ├── PipelineMetagenomeCommunities.py ├── PipelinePeakcalling.py ├── PipelineRrbs.py ├── PipelineTimeseries.py ├── PipelineTranscriptDiffExpression.py ├── PipelineTransfacMatch.py ├── metapipeline_medip.py ├── metapipeline_medip │ ├── conf.py │ ├── pipeline.ini │ └── sphinxreport.ini ├── pipeline_ancestral_repeats.py ├── pipeline_ancestral_repeats │ ├── pipeline.ini │ └── sphinxreport.ini ├── pipeline_annotations.py ├── pipeline_annotations.py~master ├── pipeline_annotations │ ├── pipeline.ini │ └── sphinxreport.ini ├── pipeline_benchmark_rnaseqmappers.py ├── pipeline_benchmark_rnaseqmappers │ ├── pipeline.ini │ └── sphinxreport.ini ├── pipeline_capseq.py ├── pipeline_chains.py ├── pipeline_chains │ ├── pipeline.ini │ └── sphinxreport.ini ├── pipeline_chipseq.py ├── pipeline_chipseq │ ├── pipeline.ini │ └── sphinxreport.ini ├── pipeline_cufflinks_optimization.py ├── pipeline_cufflinks_optimization │ └── pipeline.ini ├── pipeline_expression.py ├── pipeline_expression │ └── sphinxreport.ini ├── pipeline_fastqToBigWig.py ├── pipeline_fusion.py ├── pipeline_fusion │ ├── pipeline.ini │ └── sphinxreport.ini ├── pipeline_genesets.py ├── pipeline_genesets │ └── pipeline.ini ├── pipeline_genomeassembly │ └── pipeline.ini ├── pipeline_idr.py ├── pipeline_idr │ ├── pipeline.ini │ └── sphinxreport.ini ├── pipeline_liftover.py ├── pipeline_liftover │ ├── pipeline.ini │ └── sphinxreport.ini ├── pipeline_mappability.py ├── pipeline_mappability │ └── pipeline.ini ├── pipeline_mapping_benchmark.py ├── pipeline_mapping_benchmark │ ├── pipeline.ini │ └── sphinxreport.ini ├── pipeline_medip.py ├── pipeline_medip │ ├── pipeline.ini │ └── sphinxreport.ini ├── pipeline_metagenomecommunities.py ├── pipeline_metagenomecommunities │ └── pipeline.ini ├── pipeline_peakcalling.py ├── pipeline_peakcalling │ ├── pipeline.ini │ └── sphinxreport.ini ├── pipeline_polyphen.py ├── pipeline_polyphen │ ├── conf.py │ ├── pipeline.ini │ └── sphinxreport.ini ├── pipeline_proj020.py ├── pipeline_promotors.py ├── pipeline_promotors │ ├── pipeline.ini │ └── sphinxreport.ini ├── pipeline_rnaseq.py ├── pipeline_rnaseq │ ├── __init__.py │ ├── analysis.rst │ ├── conf.py │ ├── contents.rst │ ├── pipeline.ini │ ├── pipeline.rst │ ├── pipeline │ │ ├── CodingTranscription.rst │ │ ├── CufflinksResults.rst │ │ ├── DESeqResults.rst │ │ ├── DifferentialExpressionComparison.rst │ │ ├── DifferentialGeneExpression.rst │ │ ├── Export.rst │ │ ├── ExpressionLevels.rst │ │ ├── GeneExpression.rst │ │ ├── GeneExpressionConfidence.rst │ │ ├── GeneExpressionFPKM.rst │ │ ├── GeneExpressionRealEstate.rst │ │ ├── GeneModels.rst │ │ ├── GeneModelsBenchmark.rst │ │ ├── GeneModelsFinalMappability.rst │ │ ├── GeneModelsFinalSummary.rst │ │ ├── GeneModelsFinalSummary.st │ │ ├── GeneModelsGeneSet.rst │ │ ├── GeneModelsReproducibility.rst │ │ ├── GeneModelsSummary.rst │ │ ├── GeneModelsTranscripts.rst │ │ ├── Mapping.rst │ │ ├── MappingAlignmentStatistics.rst │ │ ├── MappingContext.rst │ │ ├── MappingProcess.rst │ │ ├── MappingReads.rst │ │ ├── Methods.rst │ │ ├── NoncodingTranscription.rst │ │ ├── ReferenceCoverage.rst │ │ ├── Status.rst │ │ ├── TranscriptModelling.rst │ │ └── Validation.rst │ ├── sphinxreport.ini │ ├── trackers │ │ ├── DifferentialExpression.py │ │ ├── Expression.py │ │ ├── Genemodels.py │ │ ├── Lincrna.py │ │ ├── Mapping.py │ │ ├── QC.py │ │ ├── Reference.py │ │ ├── RnaseqReport.py │ │ ├── Status.py │ │ ├── Validation.py │ │ └── __init__.py │ └── usage.rst ├── pipeline_rnaseqlncrna.py ├── pipeline_rnaseqlncrna │ ├── README-CGAT │ ├── pipeline.ini │ └── sphinxreport.ini ├── pipeline_rnaseqtranscripts.py ├── pipeline_rnaseqtranscripts │ ├── pipeline.ini │ └── sphinxreport.ini ├── pipeline_rrbs.py ├── pipeline_rrbs │ ├── pipeline.ini │ └── sphinxreport.ini ├── pipeline_timeseries.py ├── pipeline_timeseries │ └── pipeline.ini ├── pipeline_transcriptdiffexpression.py ├── pipeline_transcriptdiffexpression │ ├── contents.rst │ ├── pipeline.ini │ ├── pipeline.rst │ ├── pipeline │ │ ├── Biotypes.rst │ │ ├── Exploration.rst │ │ ├── ExpressionTables.rst │ │ ├── Results.rst │ │ ├── Simulation.rst │ │ ├── SleuthDiagnostics.rst │ │ └── Summary.rst │ └── trackers │ │ ├── Isoform.py │ │ ├── IsoformReport.py │ │ ├── Results.py │ │ ├── Simulations.py │ │ └── __init__.py ├── pipeline_transcriptome.py ├── pipeline_transcriptome │ ├── pipeline.ini │ └── sphinxreport.ini ├── pipeline_transfacmatch.py ├── pipeline_transfacmatch │ └── pipeline.ini ├── pipeline_variant_annotation.changelog ├── pipeline_variant_annotation.py ├── pipeline_variant_annotation │ └── sphinxreport.ini ├── pipeline_variants.py ├── pipeline_variants │ ├── pipeline.ini │ └── sphinxreport.ini └── reports │ ├── pipeline_capseq │ ├── Makefile │ ├── contents.rst │ ├── pipeline.rst │ ├── pipeline │ │ ├── IntervalsByAvgVal.rst │ │ ├── IntervalsByCDSOverlap.rst │ │ ├── IntervalsByFoldChange.rst │ │ ├── IntervalsByLength.rst │ │ ├── IntervalsByPeakVal.rst │ │ ├── Mapping.rst │ │ ├── Methods.rst │ │ ├── genome_composition.rst │ │ ├── macs.rst │ │ ├── macs_annotations.rst │ │ ├── macs_cgi_intervals.rst │ │ ├── macs_diagnostics.rst │ │ ├── macs_genomic_features.rst │ │ ├── macs_interval_comparison.rst │ │ ├── macs_intervals.rst │ │ ├── macs_long_intervals.rst │ │ ├── macs_low_cpg_intervals.rst │ │ ├── macs_parameter_correlation.rst │ │ ├── macs_replicated_genes_with_nmi.rst │ │ ├── macs_replicated_interval_genomic_features.rst │ │ ├── macs_replicated_interval_noncoding.rst │ │ ├── macs_replicated_interval_rnaseq_tss.rst │ │ ├── macs_replicated_interval_tss_distance.rst │ │ ├── macs_replicated_intervals.rst │ │ ├── macs_replicated_intervals_per_contig.rst │ │ ├── macs_replicated_shared_intervals.rst │ │ ├── macs_replicated_tissue_specific_intervals.rst │ │ ├── macs_replicated_unique_interval_chromatin_profile.rst │ │ ├── macs_replicated_unique_intervals.rst │ │ ├── macs_shared_intervals.rst │ │ ├── macs_tss_distance.rst │ │ ├── macs_tss_intervals.rst │ │ ├── macs_unique_intervals.rst │ │ ├── peakshape.rst │ │ └── predicted_cgis.rst │ ├── server.py │ └── trackers │ │ ├── Mapping.py │ │ ├── cpgReport.py │ │ ├── genome_composition.py │ │ ├── macs.py │ │ ├── macs_annotations.py │ │ ├── macs_cgi_intervals.py │ │ ├── macs_genomic_features.py │ │ ├── macs_genomic_locations.py │ │ ├── macs_interval_comparison.py │ │ ├── macs_interval_lists.py │ │ ├── macs_intervals.py │ │ ├── macs_parameter_correlation.py │ │ ├── macs_replicated_genes_with_nmi.py │ │ ├── macs_replicated_interval_annotations.py │ │ ├── macs_replicated_interval_comparison.py │ │ ├── macs_replicated_interval_genomic_features.py │ │ ├── macs_replicated_interval_noncoding.py │ │ ├── macs_replicated_interval_rnaseq_tss.py │ │ ├── macs_replicated_interval_tss_distance.py │ │ ├── macs_replicated_intervals.py │ │ ├── macs_replicated_intervals_per_contig.py │ │ ├── macs_replicated_shared_intervals.py │ │ ├── macs_replicated_tissue_specific_intervals.py │ │ ├── macs_replicated_unique_interval_chromatin_profile.py │ │ ├── macs_replicated_unique_intervals.py │ │ ├── macs_shared_intervals.py │ │ ├── macs_tss_distance.py │ │ ├── macs_tss_intervals.py │ │ ├── macs_unique_intervals.py │ │ ├── peakshape.py │ │ └── predicted_cgis.py │ ├── pipeline_chipseq │ ├── __init__.py │ ├── analysis.rst │ ├── contents.rst │ ├── pipeline.rst │ ├── pipeline │ │ ├── Annotations.rst │ │ ├── Binding.rst │ │ ├── Correlations.rst │ │ ├── IntervalLists.rst │ │ ├── Intervals.rst │ │ ├── Mapping.rst │ │ ├── Methods.rst │ │ ├── Motifs.rst │ │ ├── MotifsAbInitio.rst │ │ ├── MotifsBioProspector.rst │ │ ├── MotifsCorrelations.rst │ │ ├── MotifsGlam.rst │ │ ├── MotifsKnown.rst │ │ ├── MotifsMASTCurves │ │ ├── MotifsTSS.rst │ │ ├── Overlaps.rst │ │ ├── PeakCalling.rst │ │ ├── Peaks.rst │ │ ├── Repeats.rst │ │ ├── Reproducibility.rst │ │ └── TSS.rst │ ├── python │ │ └── Overlaps.py │ ├── trackers │ │ ├── Annotations.py │ │ ├── Annotator.py │ │ ├── BioProspector.py │ │ ├── ChipseqReport.py │ │ ├── Distances.py │ │ ├── Expression.py │ │ ├── Intervals.py │ │ ├── Manuscript.py │ │ ├── Mapping.py │ │ ├── Motifs.py │ │ ├── MotifsTSS.py │ │ ├── Nubiscan.py │ │ ├── Overlaps.py │ │ ├── PeakCalling.py │ │ ├── ReadsUnderPeaks.py │ │ ├── RegionsOfInterest.py │ │ ├── Repeats.py │ │ ├── SNP.py │ │ ├── Status.py │ │ ├── TSS.py │ │ ├── Tracks.py │ │ └── Transcripts.py │ └── usage.rst │ ├── pipeline_idr │ ├── __init__.py │ ├── analysis.rst │ ├── contents.rst │ ├── pipeline.rst │ ├── pipeline │ │ ├── inter_replicate.rst │ │ ├── peak_calling.rst │ │ ├── pooled_pseudoreplicate.rst │ │ └── pseudo_replicate.rst │ └── trackers │ │ └── IDR.py │ ├── pipeline_peakcalling │ ├── __init__.py │ ├── contents.rst │ ├── pipeline │ │ ├── Annotations.rst │ │ ├── Binding.rst │ │ ├── Callers.rst │ │ ├── Correlations.rst │ │ ├── Encode.rst │ │ ├── Export.rst │ │ ├── IDR.rst │ │ ├── IntervalLists.rst │ │ ├── IntervalsPeaks.rst │ │ ├── IntervalsRegions.rst │ │ ├── IntervalsSummits.rst │ │ ├── MACS.rst │ │ ├── MACS2.rst │ │ ├── Mapping.rst │ │ ├── Methods.rst │ │ ├── Overlaps.rst │ │ ├── Peaks.rst │ │ ├── Reproducibility.rst │ │ ├── SICER.rst │ │ ├── SPP.rst │ │ ├── Status.rst │ │ └── TSS.rst │ ├── trackers │ │ ├── Annotations.py │ │ ├── Distances.py │ │ ├── Intervals.py │ │ ├── Mapping.py │ │ ├── Overlaps.py │ │ ├── PeakCalling.py │ │ ├── PeakcallingReport.py │ │ ├── ReadsUnderPeaks.py │ │ ├── Status.py │ │ ├── TSS.py │ │ └── Tracks.py │ └── usage.rst │ └── pipeline_peakcalling_obsolete │ ├── __init__.py │ ├── contents.rst │ ├── pipeline │ ├── Annotations.rst │ ├── Binding.rst │ ├── Callers.rst │ ├── Correlations.rst │ ├── Encode.rst │ ├── Export.rst │ ├── IDR.rst │ ├── IntervalLists.rst │ ├── IntervalsPeaks.rst │ ├── IntervalsRegions.rst │ ├── IntervalsSummits.rst │ ├── MACS.rst │ ├── MACS2.rst │ ├── Mapping.rst │ ├── Methods.rst │ ├── Overlaps.rst │ ├── Peaks.rst │ ├── Reproducibility.rst │ ├── SICER.rst │ ├── SPP.rst │ ├── Status.rst │ └── TSS.rst │ ├── trackers │ ├── Annotations.py │ ├── Distances.py │ ├── Intervals.py │ ├── Mapping.py │ ├── Overlaps.py │ ├── PeakCalling.py │ ├── PeakcallingReport.py │ ├── ReadsUnderPeaks.py │ ├── Status.py │ ├── TSS.py │ └── Tracks.py │ └── usage.rst ├── requires.txt ├── scripts ├── __init__.py ├── bashrc.cgat ├── cgat_build_report_page.py ├── cgat_check_deps.py ├── cgat_clean.py ├── cgat_cluster_distribute.py ├── cgat_conda_deps.sh ├── cgat_cwd2list.py ├── cgat_file_apply.sh ├── cgat_logfiles2tsv.py ├── cgat_ruffus_profile.py ├── cgat_tsv2links.py ├── cgat_zap.py ├── conda.py ├── coverage.r ├── cpc.sh ├── csort ├── farm.py ├── get_testing_regexes.sh ├── gff_sort ├── hsort ├── match_conda_deps.sh ├── merge_conda_deps.sh ├── merge_testing_output.sh ├── nofarm.py ├── qkill.py ├── run.py ├── run_function.py ├── secs2hours.sh ├── submit.py └── version.py ├── setup.py ├── test_all.sh ├── tests ├── option_list.tsv ├── test_commandline.py ├── test_import.py ├── test_scripts.py └── test_style.py └── tox.ini /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/CGATOxford/CGATPipelines/HEAD/.gitignore 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