Files in HiCcompare

HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets

README.md R/make_InteractionSet.R R/plot_functions.R R/hic_loess.R R/Cournac_normalization.R R/get_CNV.R R/create_hic_table.R R/nhek.IS.R R/hic_diff.R R/volcano.R R/brain_table.R R/HiCcompare.r R/HMEC.chr10.R R/MA_norm.R R/hicpro2bedpe.R R/hmec.IS.R R/centromere_locations.R R/NHEK.chr10.R R/NHEK.chr22.R R/KRnormalization.R R/visualize_pvals.R R/matrix_transformations.R R/hic_simulate.R R/hic_compare.R R/hg19_blacklist.R R/total_sum.R R/filter_params.R R/remove_centromere.R R/cooler.R R/cooler2bedpe.R R/manhattan_plot.R R/HMEC.chr22.R R/split_centromere.R R/hg38_blacklist.R R/sim_matrix.R vignettes/HiCcompare-vignette.Rmd man/cooler.Rd man/sim.other.methods.Rd man/hic_simulate.Rd man/hg38_blacklist.Rd man/sparse2full.Rd man/sim_matrix.Rd man/centromere_locations.Rd man/filter_params.Rd man/HMEC.chr10.Rd man/HMEC.chr22.Rd man/hic_compare.Rd man/nhek.IS.Rd man/hg19_blacklist.Rd man/hic_loess.Rd man/create.hic.table.Rd man/MD.plot2.Rd man/cooler2sparse.Rd man/hic_diff.Rd man/brain_table.Rd man/MD.plot1.Rd man/total_sum.Rd man/MA_norm.Rd man/KRnorm.Rd man/split_centromere.Rd man/NHEK.chr10.Rd man/SCN.Rd man/manhattan_plot.Rd man/get_CNV.Rd man/visualize_pvals.Rd man/full2sparse.Rd man/HiCcompare-package.Rd man/cooler2bedpe.Rd man/NHEK.chr22.Rd man/hmec.IS.Rd man/remove_centromere.Rd man/hicpro2bedpe.Rd man/make_InteractionSet.Rd tests/testthat.R tests/testthat/test_matrix_transformations.R tests/testthat/test_hic_loess_input.R tests/testthat/test_pipeline_works.R tests/testthat/test_create_hic_table.R inst/doc/HiCcompare-vignette.R inst/doc/HiCcompare-vignette.Rmd