API for robinweide/GENOVA
GENOVA: expore the Hi-C
| Global functions | |
|---|---|
| .build_triangle_edge | Source code |
| .check_disco_attr | Source code |
| .check_disco_classes | Source code |
| .check_disco_resolutions | Source code |
| .check_disco_slots | Source code |
| .choose_palette | Source code |
| .clip_edge | Source code |
| .clip_poly | Source code |
| .core_pyramid | Source code |
| .main_data | Source code |
| .main_data.domainogram_discovery | Source code |
| .main_data.genomescore_discovery | Source code |
| .merge_array_slot | Source code |
| .metric_name | Source code |
| .metric_name.CS_discovery | Source code |
| .metric_name.DI_discovery | Source code |
| .metric_name.IS_discovery | Source code |
| .metric_name.virtual4C_discovery | Source code |
| .remap_layer_aes | Source code |
| .resolve_colour | Source code |
| .set_facet_factorlevel | Source code |
| .slice_layer | Source code |
| .transform_xy_coords | Source code |
| .update_manual_scale | Source code |
| APA | Man page Source code |
| ARA | Man page Source code |
| ATA | Man page Source code |
| CSCAn | Man page Source code |
| GENOVA | Man page |
| GENOVA-package | Man page |
| GENOVA_THEME | Source code |
| GENOVA_colour_scales | Man page |
| GENOVA_colours | Man page |
| GENOVA_image | Man page |
| HiCseg.callTAD | Man page Source code |
| PESCAn | Man page Source code |
| RCP | Man page Source code |
| RCPchrom | Source code |
| RCPlfc | Man page |
| `[.anchors` | Source code |
| `expnames<-.ARMLA_discovery` | Source code |
| `expnames<-.RCP_discovery` | Source code |
| `expnames<-.chrommat_discovery` | Source code |
| `expnames<-.contacts` | Source code |
| `expnames<-.default` | Source code |
| `expnames<-.genomescore_discovery` | Source code |
| `expnames<-.saddle_discovery` | Source code |
| `expnames<-` | Source code |
| ab.polygon | Source code Source code |
| add_bed_graph | Man page Source code |
| add_bed_track | Man page Source code |
| add_ctcf_sites | Man page Source code |
| add_loops | Man page Source code |
| add_tads | Man page Source code |
| anchors | Man page |
| anchors_APA | Man page Source code |
| anchors_ARA | Man page Source code |
| anchors_ATA | Man page Source code |
| anchors_CSCAn | Man page Source code |
| anchors_PESCAn | Man page Source code |
| anchors_extendedloops | Man page Source code |
| anchors_filter_oob | Man page Source code |
| anchors_finish | Man page Source code |
| anchors_shift | Man page Source code |
| antoni | Man page |
| as.double.contacts | Source code |
| as.double.discovery | Source code |
| as.matrix.contacts_matrix | Source code |
| as_anchors | Man page Source code |
| as_track | Man page Source code |
| as_track.CS_discovery | Man page Source code |
| as_track.DI_discovery | Man page Source code |
| as_track.IS_discovery | Man page Source code |
| as_track.LayerInstance | Man page Source code |
| as_track.domainogram_discovery | Man page Source code |
| as_track.virtual4C_discovery | Man page Source code |
| bed2idx | Man page Source code |
| bundle | Man page Source code |
| bundle.ARMLA_discovery | Man page Source code |
| bundle.CS_discovery | Man page Source code |
| bundle.DI_discovery | Man page Source code |
| bundle.IIT_discovery | Man page Source code |
| bundle.IS_discovery | Man page Source code |
| bundle.RCP_discovery | Man page Source code |
| bundle.chrommat_discovery | Man page Source code |
| bundle.domainogram_discovery | Man page Source code |
| bundle.saddle_discovery | Man page Source code |
| bundle.virtual4C_discovery | Man page Source code |
| cache_chroms | Source code |
| call_TAD_insulation | Man page Source code |
| centromere.telomere.analysis | Man page Source code |
| check_compat_exp | Man page Source code |
| check_input | Source code |
| chromosome_matrix | Man page Source code |
| cis.compartment.plot | Source code |
| cis.ev | Source code |
| cis_trans | Man page Source code |
| clean_centromeres | Source code |
| compartment.score.plot | Source code |
| compartment_matrixplot | Man page Source code |
| compartment_score | Man page Source code |
| describe | Source code |
| describe_ | Source code |
| describe_.array | Source code |
| describe_.data.frame | Source code |
| describe_.data.table | Source code |
| describe_.discovery | Source code |
| describe_.list | Source code |
| describe_.matrix | Source code |
| direct_index | Man page Source code |
| discovery | Man page |
| download_GENOVA_data | Source code |
| draw.centromere.telomere | Man page Source code |
| draw.chromosome | Source code |
| draw.interarm | Source code |
| draw.loops | Source code |
| draw.tads | Source code |
| draw1loop | Source code |
| draw_exon | Source code |
| dt_matrix | Man page Source code |
| eigen.sort | Source code |
| eigen.struct | Source code |
| engine_default | Man page Source code |
| engine_flipping | Source code |
| engine_resizing | Man page Source code |
| erase_GENOVA_cache | Man page Source code |
| expnames | Man page Source code |
| expnames.ARMLA_discovery | Source code |
| expnames.IIT_discovery | Source code |
| expnames.RCP_discovery | Source code |
| expnames.chrommat_discovery | Source code |
| expnames.contacts | Source code |
| expnames.default | Source code |
| expnames.genomescore_discovery | Source code |
| expnames.list | Source code |
| expnames.saddle_discovery | Source code |
| expnames<- | Man page |
| facet_pyramid | Source code |
| features | Source code |
| fields.interp.surface | Source code |
| fillNAs | Source code |
| find_centromeres | Man page Source code |
| genomescore_as_layer | Source code |
| get.eigen | Source code |
| getEmptyCols | Source code |
| get_GENOVA_data_filepath | Source code |
| get_test_data | Man page Source code |
| ggplot_add.genomescore_discovery | Man page Source code |
| ggplot_add.mark_layer | Man page Source code |
| ggplot_add.track_layer | Man page Source code |
| gregor | Source code |
| hic_matrixplot | Man page Source code |
| image.contacts_matrix | Man page Source code |
| import_bigwig | Source code |
| insulation2heatmap | Source code |
| insulation_domainogram | Man page Source code |
| insulation_matrixplot | Man page Source code |
| insulation_score | Man page Source code |
| inter.arm.data | Source code |
| interpret_location_string | Source code |
| intra_inter_TAD | Man page Source code |
| is_anchors | Man page Source code |
| is_contacts | Source code |
| largest.stretch | Source code Source code |
| list_GENOVA_data | Source code |
| literalTRUE | Source code |
| loadCooler | Source code |
| loadHiCpro | Source code |
| loadJuicer | Source code |
| load_contacts | Man page Source code |
| log2overmean | Man page |
| log2overmedian | Man page |
| names_from_bed | Source code |
| names_from_bedpe | Source code |
| obs.exp.matrix | Source code |
| parse_rel_pos | Source code |
| parse_shape_arg | Source code |
| partition_chromosomes | Source code |
| persp.APA_discovery | Source code |
| persp.PESCAn_discovery | Source code |
| plot.APA_discovery | Man page Source code |
| plot.ARA_discovery | Man page Source code |
| plot.ATA_discovery | Man page Source code |
| plot.CSCAn_discovery | Man page Source code |
| plot.CS_discovery | Man page Source code |
| plot.DI_discovery | Man page Source code |
| plot.IIT_discovery | Man page Source code |
| plot.IS_discovery | Man page Source code |
| plot.PESCAn_discovery | Man page Source code |
| plot.RCP_discovery | Man page Source code |
| plot.bw | Source code |
| plot.domainogram_discovery | Man page Source code |
| plot.genes | Source code |
| plot.rectangle | Source code |
| plot.saddle_discovery | Man page Source code |
| plot.triangle | Source code |
| plot.virtual4C_discovery | Man page Source code |
| plot_discovery | Man page |
| print.ARMLA_discovery | Source code |
| print.CS_discovery | Source code |
| print.DI_discovery | Source code |
| print.IIT_discovery | Source code |
| print.IS_discovery | Source code |
| print.RCP_discovery | Source code |
| print.anchors | Source code |
| print.chrommat_discovery | Source code |
| print.contacts | Source code |
| print.domainogram_discovery | Source code |
| print.saddle_discovery | Source code |
| print.virtual4C_discovery | Source code |
| pyramid | Man page Source code |
| pyramid.contacts | Source code |
| pyramid.contacts_matrix | Source code |
| pyramid.default | Source code |
| pyramid.matrix | Source code |
| pyramid_difference | Man page Source code |
| pyramidannotations | Man page |
| pyramidtracks | Man page |
| quantify | Man page Source code |
| quantify.APA_discovery | Man page Source code |
| quantify.ARA_discovery | Man page Source code |
| quantify.ARMLA | Source code |
| quantify.ATA_discovery | Man page Source code |
| quantify.CSCAn_discovery | Man page Source code |
| quantify.IIT_discovery | Man page Source code |
| quantify.PESCAn_discovery | Man page Source code |
| quantify.default | Man page Source code |
| quantify.saddle_discovery | Man page Source code |
| quantify_old.APA_discovery | Source code |
| range.contacts | Source code |
| range.discovery | Source code |
| read.hicpro.matrix | Man page |
| read_bedpe | Man page Source code |
| remove.outliers | Source code |
| rep_mat_lookup | Man page Source code |
| rescale | Source code |
| resize.mat | Source code |
| resolution | Man page Source code |
| resolution.contact_matrix | Source code |
| resolution.contacts | Source code |
| resolution.default | Source code |
| resolution.discovery | Source code |
| resolution.list | Source code |
| saddle | Man page Source code |
| scale_altfill_continuous | Man page |
| scale_colour_GENOVA | Man page Source code |
| scale_colour_GENOVA_div | Man page Source code |
| scale_fill_GENOVA | Man page Source code |
| scale_fill_GENOVA_div | Man page Source code |
| select.arm | Source code |
| select.cis.arm | Source code |
| select.sub | Source code |
| select.subset.hicseg | Source code |
| select.trans.arm | Source code |
| selectData | Source code |
| selectTransData | Source code |
| select_arbitrary | Source code |
| select_subset | Man page Source code |
| shape_ARA | Source code |
| shape_TAD_checker | Source code |
| shape_TAD_cornerpeak | Source code |
| shape_TAD_insulation | Source code |
| shape_center_vs_quadrants | Source code |
| shape_center_vs_rest | Source code |
| shape_circle | Source code |
| shape_stripes | Source code |
| shuffleHiC | Man page Source code |
| sign_compartmentscore | Man page Source code |
| standardise_location | Source code |
| subset.ARMLA_discovery | Source code |
| subset.contacts | Man page Source code |
| summarise_lookup | Man page Source code |
| switch.EV | Source code |
| switch.chromosomes | Source code |
| sync_indices | Man page Source code |
| tornado_aggregate | Man page Source code |
| tornado_insulation | Man page Source code |
| trans.compartment.plot | Man page Source code |
| trans_matrixplot | Man page Source code |
| try_require | Source code |
| unbundle | Man page Source code |
| unbundle.ARMLA_discovery | Man page Source code |
| unbundle.CS_discovery | Man page Source code |
| unbundle.DI_discovery | Man page Source code |
| unbundle.IIT_discovery | Man page Source code |
| unbundle.IS_discovery | Man page Source code |
| unbundle.RCP_discovery | Man page Source code |
| unbundle.chrommat_discovery | Man page Source code |
| unbundle.domainogram_discovery | Man page Source code |
| unbundle.saddle_discovery | Man page Source code |
| unbundle.virtual4C_discovery | Man page Source code |
| uptrimat2eig | Source code |
| virtual_4C | Man page Source code |
| visualise | Man page Source code |
| visualise.APA_discovery | Man page Source code |
| visualise.ARA_discovery | Man page Source code |
| visualise.ARMLA | Source code |
| visualise.ATA_discovery | Man page Source code |
| visualise.CSCAn_discovery | Man page Source code |
| visualise.CS_discovery | Man page Source code |
| visualise.DI_discovery | Man page Source code |
| visualise.IIT_discovery | Man page |
| visualise.IS_discovery | Man page Source code |
| visualise.PESCAn_discovery | Man page Source code |
| visualise.RCP_discovery | Man page Source code |
| visualise.chrommat_discovery | Man page |
| visualise.default | Man page Source code |
| visualise.domainogram_discovery | Man page |
| visualise.saddle_discovery | Man page |
| visualise.virtual4C_discovery | Man page Source code |
| visualize | Man page |
