├── .gitignore ├── .travis.yml ├── LICENSE.txt ├── README.md ├── VERSION_HISTORY.md ├── multisample_report ├── GM12878_Rao_subset.cis_to_trans.out ├── GM12878_Rao_subset.plot_table.out ├── GM12878_Rao_subset.summary.out ├── K562_Rao.cis_to_trans.out ├── K562_Rao.plot_table.out ├── K562_Rao.summary.out ├── distanceplot_perchr.GM12878_Rao_subset.js ├── distanceplot_perchr.K562_Rao.js ├── distanceplot_perchr.test.js ├── pairsqc_report.RData ├── pairsqc_report.html ├── plots │ ├── GM12878_Rao_subset.log10prob.pdf │ ├── GM12878_Rao_subset.log10prob.png │ ├── GM12878_Rao_subset.proportion.pdf │ ├── GM12878_Rao_subset.proportion.png │ ├── K562_Rao.log10prob.pdf │ ├── K562_Rao.log10prob.png │ ├── K562_Rao.proportion.pdf │ ├── K562_Rao.proportion.png │ ├── test.log10prob.pdf │ ├── test.log10prob.png │ ├── test.proportion.pdf │ └── test.proportion.png ├── test.cis_to_trans.out ├── test.plot_table.out ├── test.summary.out ├── tsvcol.d3div_contact_frequency_vs_genomic_separation_per_chr_GM12878_Rao_subset___.tsv ├── tsvcol.d3div_contact_frequency_vs_genomic_separation_per_chr_K562_Rao___.tsv └── tsvcol.d3div_contact_frequency_vs_genomic_separation_per_chr_test___.tsv ├── out2_report ├── .cis_to_trans.out └── .plot_table.out ├── pairsqc.py ├── plot.r ├── prep_gm.sh ├── report.zip ├── report ├── distanceplot_perchr.sample.js ├── pairsqc_report.RData ├── pairsqc_report.html ├── plots │ ├── sample.log10prob.pdf │ ├── sample.log10prob.png │ ├── sample.proportion.pdf │ └── sample.proportion.png ├── sample.cis_to_trans.out ├── sample.plot_table.out ├── sample.summary.out └── tsvcol.d3div_contact_frequency_vs_genomic_separation_per_chr_sample___.tsv ├── sample1_report ├── .cis_to_trans.out ├── .plot_table.out ├── distanceplot_perchr.sample1.js ├── pairsqc_report.RData ├── pairsqc_report.html ├── plots │ ├── sample1.log10prob.pdf │ ├── sample1.log10prob.png │ ├── sample1.proportion.pdf │ └── sample1.proportion.png ├── sample1.cis_to_trans.out ├── sample1.plot_table.out ├── sample1.summary.out └── tsvcol.d3div_contact_frequency_vs_genomic_separation_per_chr_sample1___.tsv ├── sample_command.sh ├── test_samples ├── GRCh37.chrom.sizes.mainonly ├── GRCh37.chrom.sizes.mainonly.female ├── GRCh37.chrom.sizes.mainonly:1000000 ├── hg19.chrom.sizes ├── merged_nodup.tab.chrblock_sorted.txt.gz └── merged_nodup.tab.chrblock_sorted.txt.gz.px2 ├── tests └── test.sh ├── tst_report.zip └── tst_report ├── distanceplot_perchr.tst.js ├── pairsqc_report.RData ├── pairsqc_report.html ├── plots ├── tst.log10prob.pdf ├── tst.log10prob.png ├── tst.proportion.pdf └── tst.proportion.png ├── tst.cis_to_trans.out ├── tst.plot_table.out ├── tst.summary.out └── tsvcol.d3div_contact_frequency_vs_genomic_separation_per_chr_tst___.tsv /.gitignore: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /.travis.yml: 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