Related Issues (20)
- [Suggestion] Read in custom architecture and loss functions from command line HOT 1
- Add an option to predict allowing for a bed file of regions to predict
- Interpretation failing due to old deepLIFT version
- interpret saves h5 files extremely slowly HOT 2
- [suggestion] Remove --stranded and --has-control flags; infer these from input_data.json
- Integrate new batch generator that combines foreground and background loci
- Update modisco version HOT 2
- Add hit scoring feature as new command
- Test if shap is working fine for all newly created models
- Test entire pipeline for TF models
- Test entire pipeline for chromatin models
- using tensorflow 2
- shap scores for multi-task
- parameter tweaking for Dnase/ATAC-seq data HOT 1
- Installation fails due to tensorflow requirement HOT 1
- shap_scores aren't compatible with non-bias models
- Training step fails with undefined variable 'chroms'
- bug in Counts Pearson metric
- Option to set number of dilated layers (and sanity check for architecture) HOT 3
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