shaman-package | shaman. |
ctcf_forward | Human CTCF motifs found on forward strand on hg19 genome |
ctcf_reverse | Human CTCF motifs found on reverse strand on hg19 genome |
get_param | Get params from saved var |
get_param_list | Get params from saved var |
init_params | Read params from files |
shaman | shaman. |
shaman_generate_feature_grid | Calculate spatial enrichment of contacts between two features |
shaman_get_test_track_db | returns test misha db |
shaman_gplot_map | plot an observed or expected hic map |
shaman_gplot_map_score | plot a normlized hic map |
shaman_kk_norm | Compute a score matrix for observed data based on the expected for a given set of points |
shaman_plot_feature_grid | Plot spatial enrichment of contacts between two features |
shaman_plot_map_score_with_annotations | plots hic normalized map with annotations |
shaman_plot_tracks_and_annotations | plots misha 1D tracks and annotations |
shaman_score_hic_mat | generate a score matrix for observed data based on the expected for a given 2D focus interval |
shaman_score_hic_mat_for_track | generate a score matrix for observed data based on the expected |
shaman_score_hic_points | generate a score matrix for observed data based on the expected for a given set of points |
shaman_score_hic_track | generate a score hic track based on observed and expected (shuffled) hic data |
shaman_score_pal | Returns the color palette used to display normalized scores |
shaman_shuffle_and_score_hic_mat | Inline function for generating an expected matrix and computing the score for a given interval |
shaman_shuffle_hic_mat_for_track | Generate an expected matrix from observed data as a process for generating an expected track |
shaman_shuffle_hic_track | generate an expected hic track based on observed hic data |