Man pages for haizi-zh/hictools
Home-made handy tools for Hi-C
| allowed_resol | Get a list of all allowed resolutions |
| compartment_fanc | Get compartment using FANC, from an existing .hic file |
| compartment_ht | Compute compartment scores using hictools's own... |
| compartment_juicer_file | Compute compartment scores using Juicer tools, from an... |
| comp_correlation | Calculate correlation coefficients between two compartment... |
| concat_hic | Concatenate a list of 'ht_table' |
| convert_hic_matrix | Convert a Hi-C map to a naive matrix |
| decay | Apply a "decay curve" to a Hi-C matrix |
| gc.GRCh37.100kbp | GC content |
| gencode.v30.b37.gene_density.50kbp | Gene density |
| get_compartment | Calculate compartment scores using Juicer tools |
| get_compartment.character | Calculate compartment scores |
| get_compartment.ht_table | Calculate compartment scores |
| get_juicer_tools | Return the path of juicer_tools which is shipped along with... |
| hicexplorer_pca | Run hicPCA |
| hic_genome | Get Hi-C genome |
| hic_genome-set | Set Hi-C genome |
| hic_norm | Get Hi-C normalization method |
| hic_norm-set | Set Hi-C normalization method |
| hic_resol | Get Hi-C resolution |
| hic_sample | Get Hi-C sample name |
| hic_sample-set | Set Hi-C sample name |
| hic_type | Get Hi-C data type |
| hic_type-set | Set Hi-C data type |
| ht_table | Construct an 'ht_table' object, which represents a Hi-C-like... |
| is_valid_resol | Is the resolution valid? Only support a limited number of... |
| is_wholenumber | Test if 'x' is a vector of whole numbers |
| load_hic | Load Hi-C dataset from file |
| load_hic_cool | Load Hi-C data in cool format |
| load_hic_genbed | Load Hi-C data in BED format |
| load_juicer_hic | Load Hi-C dataset from a .hic file |
| normalize_hic | Normalize Hi-C matrix |
| oe_juicer | Calculate oe normalized matrix using Juicer tools |
| orient_compartment | Orient the compartment score signs according to 'reference' |
| pearson_ht | Calculate Pearson |
| pearson_juicer | Calculate O/E Pearson correlation matrix using Juicer tools |
| plot_compartment | Plot the A/B compartment profile |
| plot_compartment_scatter | Get the scatter plot between two compartment tracks |
| plot_hic_matrix | Visualize Hi-C data |
| strat_dist | Calculate distance-stratified summary |
| write_cool | Dump Hi-C data as .cool |
| write_hic | Dump Hi-C data to file |
| write_hic_bedtorch | Write the Hi-C dataset to disk in bedtorch table format |
| write_juicer_hic | Dump a Hi-C object as .hic format |
