├── GR_submit_2018 ├── G1-peak-dist.pdf ├── dREG_holdout_pr_roc_full.pdf ├── dREG_holdout_pr_roc_full.pr.png ├── dREG_holdout_pr_roc_full.roc.png ├── dhs-overlap.R ├── dregG1-DNase.png ├── dregG1-H3K27ac.png ├── dregG1-H3K27me3.png ├── dregG1-H3K4me1.png ├── dregG1-H3K4me3.png ├── dregG1-MNase.png ├── dregG1-Proseq.png ├── erna_regression.R ├── fig-1B.R ├── fig-1B.pdf ├── fig-1B0.pdf ├── fig-1C-G8trained.R ├── fig-1C-G8trained.pdf ├── fig-1C-GMtrained.R ├── fig-1C-GMtrained.pdf ├── fig-1C-demo.pdf ├── fig-1C-extendtoS.R ├── fig-1C-extendtoS.pdf ├── fig-1C-log.pdf ├── fig-1C-log2.pdf ├── fig-1C.R ├── fig-1C.pdf ├── fig-2A.R ├── fig-2A.pdf ├── fig-2B.R ├── fig-2B.pdf ├── fig-2C-v2.png ├── fig-2C-v3.png ├── fig-3A.R ├── fig-3A.pdf ├── fig-3A2.pdf ├── fig-4B-C-heterochromatin.R ├── fig-4B-logx.pdf ├── fig-4C.pdf ├── fig-5.R ├── fig-S1-corpairs.pdf ├── fig-S1-pairs.pdf ├── fig-S1.R ├── fig-S1.pdf ├── fig-S10.pdf ├── fig-S11-jaccard.pdf ├── fig-S14-PolIII.R ├── fig-S14-b.pdf ├── fig-S14-c.pdf ├── fig-S14-motif.pdf ├── fig-S14.pdf ├── fig-S2-pr-roc.R ├── fig-S4-laplace-1.pdf ├── fig-S4-laplace-2.pdf ├── fig-S4-laplace-3.pdf ├── fig-S4-laplace-4.pdf ├── fig-S4-laplace-5.pdf ├── fig-S4-laplace-old-1.pdf ├── fig-S4-laplace.R ├── fig-S4-v0.pdf ├── fig-S5.pdf ├── fig-S5D-direction.R ├── fig-S5D-uni-direction.pdf ├── fig-S6B.R ├── fig-S6B.pdf ├── fig-S7.R ├── fig-S7.pdf ├── fig-S8-2.pdf ├── fig-S8.R ├── fig-S8.pdf ├── fig-S8a.pdf ├── fig-S8b.pdf ├── fig-S9-x.pdf ├── fig-S9.R ├── fig-S9.pdf ├── fig-S9A.R ├── fig-S9A.pdf ├── fig-U-G1-peak-dist.pdf ├── fig-U1-dist.pdf ├── fig-U1.R ├── fig-U2.R ├── fig-U2.pdf ├── fig-laplace-5.pdf ├── fig-laplace.R ├── fig-pr-roc.R ├── gateway-figures.zip ├── heatmap-mnaseq.R ├── heatmap-proseq.R ├── heatmaps.R ├── histone-dreg-v2.png ├── jaccard.pdf ├── levelplot2.R ├── metaplot.R ├── novel-tres.R ├── roc.boot.pdf ├── roc.curve.pdf └── tf-overlap.R ├── Makefile ├── README.md ├── bed_merge.pl ├── dREG-manual.pdf ├── dREG ├── DESCRIPTION ├── Makefile.dREG ├── NAMESPACE ├── R │ ├── bigwig_check.R │ ├── eval_svm.R │ ├── get_informative_positions.R │ ├── get_test_set.R │ ├── peak_calling.R │ ├── peak_calling_ext.R │ ├── peak_calling_rf.R │ ├── read_genomic_data.R │ ├── roc.calc.R │ ├── train_svm.R │ └── zzz.R ├── README.md ├── inst │ └── extdata │ │ └── rf-model-201803.RDS ├── man │ ├── check_bigwig.Rd │ ├── combine.roc.Rd │ ├── eval_reg_svm.Rd │ ├── genomic_data_model.Rd │ ├── get_informative_positions.Rd │ ├── get_test_set.Rd │ ├── logreg.roc.calc.Rd │ ├── peak_calling.Rd │ ├── read_genomic_data.Rd │ ├── regulatory_svm.Rd │ ├── roc.auc.Rd │ ├── roc.calc.Rd │ └── roc.plot.Rd └── src │ ├── Makevars │ ├── bigWigpath.R │ ├── read_genomic_data.c │ └── read_genomic_data.h ├── dREG_paper_analyses ├── bed_merge.pl ├── figures │ ├── Supp.Fig.3.R │ ├── fig1.R │ ├── fig3.R │ ├── fig3a.R │ ├── fig3a.bsh │ ├── fig3c.R │ ├── histplot.R │ └── plot.gdm.R ├── getEnrichmentOfInfPos.bsh ├── optmize_model_size.complexity.R ├── roundBedGraph.bsh ├── testAccuracy │ ├── bed_merge.pl │ └── testAccuracy.bsh ├── test_get_data.R ├── test_get_informative_positions.R ├── train_nn │ ├── deep_generative_model.R │ ├── get_test_files │ │ ├── MetaPlotPolyA.R │ │ ├── setupTrainingFiles.bsh │ │ ├── stepup.R │ │ └── txn.strand.R │ ├── test_train_dbn.R │ ├── test_train_nnet.R │ ├── train_dbn.dnase.R │ └── train_dbn.dnase.sh ├── train_svm │ ├── bed_merge.pl │ ├── compare_to_cage │ │ └── getCage.R │ ├── eqtl │ │ ├── GetDiseaseAssocSnps.py │ │ ├── cmp_classes.bsh │ │ ├── cmp_disease_assoc_snps.bsh │ │ ├── gm12878.eqtl.enrichment.R │ │ ├── prep_files.sh │ │ └── residual_enrichment.bsh │ ├── erna_regression │ │ ├── cmpEnhProm.R │ │ ├── elf1.binding.titrateDHS.bsh │ │ ├── erna_drawbars.R │ │ ├── erna_randomForest.R │ │ ├── erna_regression.R │ │ ├── genomeScan.R │ │ ├── genomeScan.bsh │ │ ├── getRatios.R │ │ ├── jaspar.format.txt │ │ ├── makePIQ_starch.bsh │ │ ├── openchromatin_regression.R │ │ ├── runPIQ.bsh │ │ ├── setup.PIQ.R │ │ └── setup.erna_regression.bsh │ ├── optimize_svm_reg_model.R │ ├── phylo_conservation │ │ ├── phyloP.R │ │ ├── runInsight.bsh │ │ └── runInsightFunction.bsh │ ├── run_svm │ │ ├── scan_ac16.R │ │ ├── scan_ac16.sh │ │ ├── scan_additional_time_points.R │ │ ├── scan_cd4-h1.R │ │ ├── scan_cd4-h1.sh │ │ ├── scan_galGal.R │ │ ├── scan_galGal.sh │ │ ├── scan_gm12878.R │ │ ├── scan_gm12878.sh │ │ ├── scan_hela.R │ │ ├── scan_hela.sh │ │ ├── scan_imr90.R │ │ ├── scan_imr90.sh │ │ ├── scan_k562.R │ │ ├── scan_k562.sh │ │ ├── scan_k562_small.R │ │ ├── scan_k562_small.sh │ │ ├── scan_mcf7.40m.R │ │ ├── scan_mcf7.40m.sh │ │ ├── scan_mcf7.R │ │ ├── scan_mcf7.sh │ │ ├── venn.R │ │ └── venn.bsh │ ├── testSensSpecPipeline.bsh │ ├── testSensSpecPipeline.gm12878.bsh │ ├── test_train_p-svm.R │ ├── test_train_svm.R │ ├── test_train_svm_auto.R │ ├── train_svm.R │ ├── train_svm.dnase.R │ ├── train_svm.dnase.sh │ ├── train_svm.sh │ ├── venn │ │ ├── H3K27ac-iRNA.bsh │ │ ├── getAssayOverlaps.bsh │ │ ├── getCompartmentChangesBetweenCells.R │ │ ├── getCompartmentChangesBetweenCells.bsh │ │ ├── getOverlappingTFs.bsh │ │ ├── histoneMods.overlaps.MetOverlaps.R │ │ ├── histoneMods.overlaps.bsh │ │ ├── venn.R │ │ ├── venn.bsh │ │ └── whats.in.exclusive.dnase.or.chromhmm.loci.bsh │ └── writeBed.bsh └── validation │ ├── auto_subsample.sh │ └── generic_subsample.py ├── dreg-gateway.png ├── example ├── GM12878.negative.bed.rdata ├── GM12878.positive.bed.rdata ├── K562.chr21.minus.bw ├── K562.chr21.plus.bw ├── k562.negative.bed.rdata └── k562.positive.bed.rdata ├── gateway-update.md ├── gr-submit-codes.tar.gz ├── rDeps.R ├── run_dREG.R ├── run_dREG.bsh ├── run_predict.R ├── run_predict.bsh ├── test ├── bash_test.bsh ├── benchmark.r ├── perform_comparsion.pdf └── read_genomic_data_test.r └── writeBed.bsh /GR_submit_2018/G1-peak-dist.pdf: -------------------------------------------------------------------------------- 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