Package index • shaman

Data processing
`shaman_shuffle_hic_track()`	Generate an expected hic track based on observed hic data
`shaman_shuffle_hic_mat_for_track()`	Generate an expected matrix from observed data as a process for generating an expected track
`shaman_score_hic_track()`	Generate a score hic track based on observed and expected (shuffled) hic data
`shaman_score_hic_mat_for_track()`	Generate a score matrix for observed data based on the expected
`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()`	Plot a normalized hic map with annotations
`shaman_plot_tracks_and_annotations()`	Plot misha 1D tracks and annotations
`shaman_gplot_map_score()`	Plot a normalized 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
Data
`ctcf_forward`	Human CTCF motifs found on forward strand on hg19 genome
`ctcf_reverse`	Human CTCF motifs found on reverse strand on hg19 genome
configuration Parameter configuration utility functions
`shaman_get_test_track_db()`	Returns the example misha database
`get_param_list()`	Get params from saved var
`get_param()`	Get params from saved var
`init_params()`	Read params from files

Reference

Data processing

Visualization

Data

configuration