Gang Li

Missing a parameter -lrc in the tutorial

2

Hi, I am trying to follow the tutorial to train the DeepHiC model but met the following error: python data_generate.py -hr 10kb -lr 40kb -s all -chunk 40 -stride 40...

predict on new data

3

Hi, May I ask how to make predictions for the new independent data? I think it should be: _score = t(new_data_x) %*% psuper_obj$beta_dt$beta_ And they compare the score with _psuper_obj$cuts_dt_...

Hi, I have successfully run psupertime on multiple datasets, but I met a weird error for a new dataset: ``` cross-validation training, 5 folds: fold 1 Error in lognet(xd, is.sparse,...

Scalability

1

Nice work! Can it handle 1 million samples with 2k or 20k features? Do you foresee any limitations if I use the Python version for this task?

I notice each time the visualize function might generate a different UMAP plot due to the random state being not fixed. Could you add the default random seed similar to...

Hi, In visualization.py (line 13), the styles is defined as: `styles = ['g', 'r', 'b', 'y', 'k', 'm', 'c', 'greenyellow', 'lightcoral', 'teal'] ` So we try to run: `Pa.Visualize(data, integrated_data,...