Issues

• Bias model for single-end bulk ATAC-seq

  kundajelab/chrombpnet#283 · Filter by author snaqvi1990 opened on Jul 2, 2026
  1

• Invalid interval bounds while generaing prediction bigwigs

  kundajelab/chrombpnet#281 · Filter by author GalinaKoksharova opened on May 18, 2026
  1

• Potential impact of shift mismatch between bias model and training sample

  kundajelab/chrombpnet#280 · Filter by author ypauling opened on May 17, 2026

• can you update the tensorflow vesion

  kundajelab/chrombpnet#279 · Filter by author BenxiaHu opened on Apr 10, 2026
  1

• Non-standard enzyme shift (+4/+4) when running ChromBPNet on cell-type subsetted SHARE-seq fragments

  kundajelab/chrombpnet#278 · Filter by author kgmuelle opened on Mar 26, 2026

• Support cross-species training and prediction?

  kundajelab/chrombpnet#277 · Filter by author 09oulin opened on Mar 22, 2026

• CPU usage in chrombpnet

  kundajelab/chrombpnet#276 · Filter by author conniecl opened on Mar 18, 2026

• Bias Model pearsonR<-0.5

  kundajelab/chrombpnet#275 · Filter by author LabMiceNoveda opened on Mar 4, 2026
  2

• Can predicted scores for a specific region from different models be comparable?

  kundajelab/chrombpnet#274 · Filter by author 09oulin opened on Mar 3, 2026

• Flanks of motif CWMs from chrombpnet model are rich in GCs?

  kundajelab/chrombpnet#272 · Filter by author 09oulin opened on Feb 24, 2026
  5

• DNase peak calling

  kundajelab/chrombpnet#271 · Filter by author cybluetree opened on Jan 18, 2026

• Clarification on ChromBPNet Tracks Used in Extended Fig. 2B

  kundajelab/chrombpnet#270 · Filter by author tristan-ka opened on Dec 10, 2025
  1

• auxiliary/modisco_results_counts_scores.h5 and evaluation/modisco_counts missing

  kundajelab/chrombpnet#269 · Filter by author YinLabTJ opened on Dec 2, 2025

• ChromBPNet or BPNet for CUT&Tag?

  kundajelab/chrombpnet#268 · Filter by author zhang-jiankun opened on Nov 24, 2025

• splitting the non-GPU taks.

  kundajelab/chrombpnet#267 · Filter by author okurman opened on Nov 2, 2025
  1

• Merging peaks for sample comparisons

  kundajelab/chrombpnet#266 · Filter by author samfenske opened on Oct 31, 2025

• DNase-seq bias training: “Input file shifts inconsistent”

  kundajelab/chrombpnet#264 · Filter by author ashx56 opened on Oct 13, 2025

• Issues using Docker image

  kundajelab/chrombpnet#263 · Filter by author sbg15236 opened on Oct 9, 2025

• Bias Pipeline stalled before training

  kundajelab/chrombpnet#262 · Filter by author sbg15236 opened on Oct 7, 2025

• TF-MoDISco motifs from counts vs. profile contributions

  kundajelab/chrombpnet#261 · Filter by author HammadFarooq opened on Sep 24, 2025

• chrombnet train hanging

  kundajelab/chrombpnet#258 · Filter by author Brawni opened on Sep 9, 2025

• what is the meaning of negative profile scores?

  kundajelab/chrombpnet#257 · Filter by author Brawni opened on Sep 6, 2025
  1

• access to pretrained models ?

  kundajelab/chrombpnet#255 · Filter by author eyes-robson opened on Aug 30, 2025
  4

• Copy number alteration correction

  kundajelab/chrombpnet#254 · Filter by author DexinYang1998 opened on Aug 22, 2025
  2

• Significant issues with cudnn bug when using H100 GPU

  kundajelab/chrombpnet#251 · Filter by author allthingsgenome opened on Aug 10, 2025