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_generate_feature_grid
                        Calculate spatial enrichment of contacts
                        between two features
shaman_get_test_track_db
                        Returns the example misha database
shaman_gplot_map        Plot an observed or expected hic map
shaman_gplot_map_score
                        Plot a normalized 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
                        Plot a normalized hic map with annotations
shaman_plot_tracks_and_annotations
                        Plot 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
