Man pages for robinweide/GENOVA
GENOVA: expore the Hi-C
| anchors | Anchors for Hi-C |
| anchors_filter_oob | Filter anchors that become out of bounds. |
| anchors_finish | Finish anchors for repeated matrix lookup |
| anchors_shift | Shift anchors |
| antoni | Antoni |
| APA | Aggregrate Peak Analysis |
| ARA | Aggregate Region Analysis |
| as_anchors | Coerce to anchors |
| ATA | Aggregate TAD analysis |
| bed2idx | Match bed-like entries to Hi-C bin indices |
| bundle | Combine discovery objects |
| call_TAD_insulation | Call TADs from insulation scores |
| centromere.telomere.analysis | centromere.telomere.analysis |
| check_compat_exp | Check compatability of a list of GENOVA experiments |
| chromosome_matrix | Chromosome matrix |
| cis_trans | Get the percentage cis-contacts genome-wide or from a region |
| compartment_matrixplot | Compartment score matrix plot |
| compartment_score | Compartment score |
| CSCAn | Cross spatial chromatin analysis |
| direct_index | Directionality index |
| discovery | Discovery class |
| draw.centromere.telomere | draw.centromere.telomere |
| dt_matrix | Upper triangle sparse symmetric triplet matrix to dense... |
| engine_default | Engine for repeated matrix lookups |
| engine_resizing | Engine for repeated matrix lookup and resizing |
| erase_GENOVA_cache | Erase cache. |
| expnames | Sample names for an object |
| find_centromeres | Empirical centromeres |
| GENOVA_colours | Colours in GENOVA |
| GENOVA_colour_scales | GENOVA gradient colour scales |
| GENOVA_image | Display a part of a Hi-C matrix |
| GENOVA-package | GENOVA: GENOVA: expore the Hi-C |
| get_test_data | Test data |
| hic_matrixplot | hic.matrixplot |
| HiCseg.callTAD | HiCseg.callTAD |
| insulation_domainogram | Domainogram of insulation |
| insulation_matrixplot | Insulation matrix plot. |
| insulation_score | Calculate insulation scores |
| intra_inter_TAD | Intra and inter TAD contacts |
| is_anchors | Test object is anchors |
| load_contacts | Construct a contacts-object. |
| log2overmean | Log 2 value over its mean |
| log2overmedian | Log 2 value over its median |
| PESCAn | Paired-end spatial chromatin analysis |
| plot_discovery | Plot discoveries |
| pyramid | Plot a region as a pyramid |
| pyramidannotations | Rotated pyramid annotations |
| pyramidtracks | Adding tracks to a pyramid plot. |
| quantify | Quantification of results |
| RCP | Relative Contact Probabilities |
| RCPlfc | RCP log2 foldchange |
| read_bedpe | Load, parse and check BEDPE. |
| read.hicpro.matrix | Read hicpro three column matrix format. |
| rep_mat_lookup | Repeated Hi-C matrix lookup |
| resolution | Get the resolution of GENOVA objects |
| saddle | Compartment versus compartment scores |
| scale_altfill_continuous | scale_altfill_continuous Makes sure no errors are returned... |
| select_subset | Get a matrix from a BED-like entry |
| shuffleHiC | Shuffle a symmetric matrix |
| sign_compartmentscore | Sign compartment score. |
| subset | subset |
| summarise_lookup | Summarise the results of a repeated matrix lookup |
| sync_indices | Synchronising indices across experiments. |
| tornado_aggregate | Tornado plot for aggregated discoveries |
| tornado_insulation | Plot a heatmap or profile of insulation scores |
| trans.compartment.plot | trans.compartment.plot |
| trans_matrixplot | Trans matrix plot |
| unbundle | Split discovery objects |
| virtual_4C | Get an average virtual 4C of 2D-regions (e.g. loops). |
| visualise | Visualise discoveries |
