basepairmodels
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kundajelab
----- for the generator 1. The input json will have new field for background loci 2. The user will specify #samples for foreground and background (-1 for all) 3. The...
1. First train bias model 2. Train main model 3. rest of the pipeline steps (shap, modisco, metrics, hit scoring)
In training two data sets with wildly different coverages, I'd like to be able to give separate counts loss weights. If I don't do that, then the data sets can...
This is just a suggestion, but I wanted to log it some place where we have a formal channel to discuss. Currently, in the input_data.json file, the user must provide...
This is the error: `File "/home/users/surag/oak/miniconda3/envs/basepairmodels/lib/python3.6/site-packages/basepairmodels/cli/interpret.py", line 192, in data_func return [dinuc_shuffle(model_inputs[0], args.num_shuffles, rng)] + \ TypeError: dinuc_shuffle() takes from 1 to 2 positional arguments but 3 were given` Followed...
The predict program currently uses input_data.json to both gather task information and get a list of peaks to predict. In the event that I want to train and predict on...
As I start complicating my interaction with BPNet more, I'd like to add a feature where the user can easily supply a network architecture and loss function to the program....
I tried to download the repo using the command `pip install --no-cache-dir --ignore-installed git+https://github.com/kundajelab/basepairmodels.git` from the README. I get the following error: ``` Collecting git+https://github.com/kundajelab/basepairmodels.git Cloning https://github.com/kundajelab/basepairmodels.git to /tmp/pip-req-build-__cioa9b Running...
the counts pearson metric saves the pearson of tracks rather than the counts
Howdy I was working through the example, and when I got to the following code snippet ``` # get coverage of 5’ positions of the plus strand bedtools genomecov -5...