deplanckelab / chromatinhd Goto Github PK

Hi,
Thanks for publishing this very useful tool!
I know this tool was developed for single-cell data, but is it possible to use it for bulk sequence data? I would be glad to hear your opinion.
Best

Thanks for releasing this method for multiome data analysis.

Is there any easy way to use ChromatinHD pred to get predictivity of a given locus with respect to a given gene, for a specific cell type? Right now, I could train individual cell type models, but that would not share information across cell types. I also see that chd.models.pred.interpret.GeneMultiWindow().score() leverages get_prediction_censored() and I could play with passing different cells to cell_ixs.

Please advise,
Kipper

Hello, I scheduled a job that trained a chromatinHD diff model which got saved in models/cutnf. Is there a functionality that lets you load this trained model given the directory name? If not can the functionality be added? Thank you!

Hi ChromatinHD team,

Congratulations on your exciting pre-print! I'm going through your tutorial, but cannot seem to import the following:

import chromatinhd.data.motifscan.download

I can't seem to find this in the github code either. Is the tutorial not updated to the most recent code (or vice versa)? Thanks so much!

Joe

Hi, I am trying to set the ChromatinHD-diff model, but getting the AttributeError: module 'chromatinhd.models.diff.model' has no attribute 'cutnf'.

The error can be resolved by importing cutnf itself 'from chromatinhd.models.diff.model import cutnf'

Hello,

Once I install the library through pip, I get the error below. I use Python3.8 on conda:

import chromatinhd
Traceback (most recent call last):
File "", line 1, in
File "/opt/anaconda3/envs/scenicplus/lib/python3.8/site-packages/chromatinhd/init.py", line 9, in
from . import loaders
File "/opt/anaconda3/envs/scenicplus/lib/python3.8/site-packages/chromatinhd/loaders/init.py", line 1, in
from .pool import LoaderPool, LoaderPool2
File "/opt/anaconda3/envs/scenicplus/lib/python3.8/site-packages/chromatinhd/loaders/pool.py", line 30, in
class LoaderPool:
File "/opt/anaconda3/envs/scenicplus/lib/python3.8/site-packages/chromatinhd/loaders/pool.py", line 34, in LoaderPool
n_todo: list[int]
TypeError: 'type' object is not subscriptable

Thanks