Man pages for tanaylab/shaman
shaman - Sampling HiC contAct Matrices for Aparametric Normalization
| ctcf_forward | Human CTCF motifs found on forward strand on hg19 genome |
| ctcf_reverse | Human CTCF motifs found on reverse strand on hg19 genome |
| dot-shaman_dump_config | Dump config file templates. |
| dot-shaman_load_config | Load all the configuration files required for the package. |
| 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... |
| 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... |
| shaman_score_hic_mat_for_track | generate a score matrix for observed data based on the... |
| shaman_score_hic_points | generate a score matrix for observed data based on the... |
| shaman_score_hic_track | generate a score hic track based on observed and expected... |
| 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... |
| shaman_shuffle_hic_mat_for_track | Generate an expected matrix from observed data as a process... |
| shaman_shuffle_hic_track | generate an expected hic track based on observed hic data |
