Data processing
shaman_shuffle_hic_track	generate an expected hic track based on observed hic data
shaman_score_hic_track	generate a score hic track based on observed and expected (shuffled) hic data
shaman_shuffle_and_score_hic_mat	Inline function for generating an expected matrix and computing the score for a given interval
shaman_score_hic_points	generate a score matrix for observed data based on the expected for a given set of points
shaman_score_hic_mat	generate a score matrix for observed data based on the expected for a given 2D focus interval
shaman_kk_norm	Compute a score matrix for observed data based on the expected for a given set of points
shaman_generate_feature_grid	Calculate spatial enrichment of contacts between two features
Visualization Methods for graphical visualizing
shaman_plot_map_score_with_annotations	plots hic normalized map with annotations
shaman_gplot_map_score	plot a normlized hic map
shaman_gplot_map	plot an observed or expected hic map
shaman_plot_feature_grid	Plot spatial enrichment of contacts between two features
shaman_score_pal	Returns the color palette used to display normalized scores
configuration Parameter configuration utility functions
shaman_get_test_track_db	returns test misha db
get_param_list	Get params from saved var
get_param	Get params from saved var
init_params	Read params from files