Files in robinweide/GENOVA
GENOVA: expore the Hi-C
.Rbuildignore
.github/ISSUE_TEMPLATE/bug_report.md
.github/ISSUE_TEMPLATE/feature_request.md
.gitignore
.travis.yml
CODE_OF_CONDUCT.md
DESCRIPTION
GENOVA.Rproj
LICENSE
NAMESPACE
NEWS.md
R/ARMLA.R
R/GENOVA.R
R/HiCseg.callTAD.R
R/RCP.R
R/call_TAD_insulation.R
R/centromere_telomere.R
R/centromeres.R
R/chromosome_matrix.R
R/cis_trans.R
R/colours.R
R/compartment_score.R
R/data.R
R/direct_index.R
R/eigen_plot.R
R/insulation_domainogram.R
R/insulation_score.R
R/intra_inter_TAD.R
R/load_contacts.R
R/loading_cooler.R
R/loading_juicer.R
R/matrixplot_compartment.R
R/matrixplot_hic.R
R/matrixplot_insulation.R
R/matrixplot_trans.R
R/methods_anchors.R
R/methods_bundeling.R
R/methods_contacts.R
R/methods_discovery.R
R/methods_expnames.R
R/methods_image.R
R/methods_matrix_lookup.R
R/methods_persp.R
R/methods_plot.R
R/methods_print.R
R/methods_quantify.R
R/methods_resolution.R
R/methods_visualise.R
R/pyramids.R
R/read_bedpe.R
R/saddle.R
R/shuffleHiC.R
R/sync_indices.R
R/test_data.R
R/tornado_aggregates.R
R/tornado_insulation.R
R/utils.R
R/virtual_4C.R
README.md
README.rmd
data/.gitignore
data/antoni.rda
inst/CITATION
man/APA.Rd
man/ARA.Rd
man/ATA.Rd
man/CSCAn.Rd
man/GENOVA-package.Rd
man/GENOVA_colour_scales.Rd
man/GENOVA_colours.Rd
man/GENOVA_image.Rd
man/HiCseg.callTAD.Rd
man/PESCAn.Rd
man/RCP.Rd
man/RCPlfc.Rd
man/anchors.Rd
man/anchors_filter_oob.Rd
man/anchors_finish.Rd
man/anchors_shift.Rd
man/antoni.Rd
man/as_anchors.Rd
man/bed2idx.Rd
man/bundle.Rd
man/call_TAD_insulation.Rd
man/centromere.telomere.analysis.Rd
man/check_compat_exp.Rd
man/chromosome_matrix.Rd
man/cis_trans.Rd
man/compartment_matrixplot.Rd
man/compartment_score.Rd
man/direct_index.Rd
man/discovery.Rd
man/draw.centromere.telomere.Rd
man/dt_matrix.Rd
man/engine_default.Rd
man/engine_resizing.Rd
man/erase_GENOVA_cache.Rd
man/expnames.Rd
man/figures/colour-divergent.png
man/figures/colour-greenpink.png
man/figures/colour-hot.png
man/figures/colour-whitered.png
man/figures/quant-ARA.png
man/figures/quant-center-vs-quandrants.png
man/figures/quant-center-vs-rest.png
man/figures/quant-checker.png
man/figures/quant-circle.png
man/figures/quant-cornerpeak.png
man/figures/quant-insulation.png
man/figures/quant-stripes.png
man/find_centromeres.Rd
man/get_test_data.Rd
man/hic_matrixplot.Rd
man/insulation_domainogram.Rd
man/insulation_matrixplot.Rd
man/insulation_score.Rd
man/intra_inter_TAD.Rd
man/is_anchors.Rd
man/load_contacts.Rd
man/log2overmean.Rd
man/log2overmedian.Rd
man/plot_discovery.Rd
man/pyramid.Rd
man/pyramidannotations.Rd
man/pyramidtracks.Rd
man/quantify.Rd
man/read.hicpro.matrix.Rd
man/read_bedpe.Rd
man/rep_mat_lookup.Rd
man/resolution.Rd
man/saddle.Rd
man/scale_altfill_continuous.Rd
man/select_subset.Rd
man/shuffleHiC.Rd
man/sign_compartmentscore.Rd
man/subset.Rd
man/summarise_lookup.Rd
man/sync_indices.Rd
man/tornado_aggregate.Rd
man/tornado_insulation.Rd
man/trans.compartment.plot.Rd
man/trans_matrixplot.Rd
man/unbundle.Rd
man/virtual_4C.Rd
man/visualise.Rd
misc/ATA_speedup_vapply.pdf
misc/ATA_speedup_vapply_vis.pdf
misc/LOGO.pdf
misc/fig1.pdf
misc/lookupTIme.R
misc/lookupTIme.pdf
misc/steppedVSarm.R
misc/steppedVSarm.pdf
misc/t1logo.jpg
vignettes/.gitignore
vignettes/GENOVA.Rmd
vignettes/GENOVA.bib
vignettes/GENOVA.pdf
vignettes/GENOVA_vignette.pdf
vignettes/logo_GENOVA.png
