Uses Supervised Learning to call TAD boundaries. One or multiple HiC-Matrices can be passed, from which a BED file will be produced containing the predicted boundary positions. By default, a EasyEnsembleClassifier as described in Liu et al.: “Exploratory Undersampling for Class-Imbalance Learning” will be used to call TADs. Internally this classifier relies on Resampling, Boosting and Bagging. Passed matrices will be range normalized by default. Alternatively, obs/exp normalization can be used. Currently, only classifiers for 10kb resolution are implemented. For building own classifiers or tune existing ones, hicTrainClassifier can be used and passed with the saved_classifer argument. A simple usage example can be seen here:

$ hicTADClassifier -m my_matrix.cool -o predictions -n range

usage: hicTADClassifier --matrices MATRICES [MATRICES ...] --out_file OUT_FILE
                        [OUT_FILE ...]
                        [--normalization_method {obs_exp,range}]
                        [--saved_classifier SAVED_CLASSIFIER]
                        [--unselect_border_cases] [--threads THREADS]
                        [--chromosomes CHROMOSOMES [CHROMOSOMES ...]] [--help]

Required arguments

--matrices, -m

HiC-Matrix file or list of files for input. Only COOLER files are supported!

--out_file, -o

output file path for predictions

Optional arguments

--normalization_method, -n

Possible choices: obs_exp, range

set the normalization mode, with which the passed matrices will be normalized. If not set, matrices will be range normalized

Default: “range”


Default classifier are available for 10kb, 25kb, 50kb and 100kb resolution. Do not set this parameter to use the default models. Pass a self-trained classifier (from hicTrainTADClassifier) to load a non-default model.


set whether genes at the border of the matrices will not be predicted

Default: False

--threads, -t

number of threads used

Default: 4


Chromosomes to include in the analysis. If not set, all chromosomes are included.


show program’s version number and exit