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python version

Status: Open.

#38 In kundajelab/basepairmodels;

· mayasheth opened on Mar 26, 2025

Training step fails with undefined variable 'chroms'

Status: Open.

#36 In kundajelab/basepairmodels;

· gregorydonahue opened on May 9, 2024

parameter tweaking for Dnase/ATAC-seq data

Status: Open.

#29 In kundajelab/basepairmodels;

· ChangxuFan opened on May 10, 2022

shap scores for multi-task

Status: Open.

#28 In kundajelab/basepairmodels;

· nzhang89 opened on May 6, 2022

Test entire pipeline for chromatin models

Status: Open.

#24 In kundajelab/basepairmodels;

· zahoorz opened on Jan 11, 2022

Test entire pipeline for TF models

Status: Open.

#23 In kundajelab/basepairmodels;

· zahoorz opened on Jan 11, 2022

Test if shap is working fine for all newly created models

Status: Open.

#22 In kundajelab/basepairmodels;

· zahoorz opened on Jan 11, 2022

Add hit scoring feature as new command

Status: Open.

#21 In kundajelab/basepairmodels;

· zahoorz opened on Jan 11, 2022

Update modisco version

Status: Open.

#20 In kundajelab/basepairmodels;

· zahoorz opened on Jan 11, 2022

Integrate new batch generator that combines foreground and background loci

enhancementNew feature or requestNew feature or request

Status: Open.

#19 In kundajelab/basepairmodels;

· zahoorz opened on Jan 11, 2022

[suggestion] Allow the user to give a counts-loss-weight value in input_data.json

Status: Open.

#15 In kundajelab/basepairmodels;

· mmtrebuchet opened on Jun 7, 2021

[suggestion] Remove --stranded and --has-control flags; infer these from input_data.json

Status: Open.

#14 In kundajelab/basepairmodels;

· mmtrebuchet opened on Jun 7, 2021