Issues

• High fraction of NaNs in cooltools.insulation when applied to Akita predicted target contact maps (sparse near-zero matrices)

  calico/basenji#224 · Filter by author Ananyajhala1 opened on Jan 28, 2026
  1

• How to reproduce Figure 5c

  calico/basenji#222 · Filter by author ahfevounccfvsa opened on Jan 22, 2026
  6

• Sliding window prediction

  calico/basenji#221 · Filter by author joachimwolff opened on Jan 15, 2026
  3

• Where can we access the pretrained mm10 model for Akita HiC prediction?

  calico/basenji#218 · Filter by author ananyapavuluri opened on Sep 26, 2025
  4

• Installation woes (Cuda, as always, is being a pain)

  calico/basenji#217 · Filter by author mmtrebuchet opened on Aug 22, 2025
  1

• Nan values and -inf during training with Akita for HiC prediction

  calico/basenji#215 · Filter by author ananyapavuluri opened on Jun 11, 2025
  1

• Poor training performance on specific cell type Hi-C data

  calico/basenji#213 · Filter by author Gemma-Zhang-326 opened on May 18, 2025
  12

• Error when running akita_train.py

  calico/basenji#205 · Filter by author xiaoxiao6630 opened on Feb 25, 2025
  1

• How to change older params.txt in manuscripts/genome_research2018 to params.json

  calico/basenji#204 · Filter by author biginfor opened on Dec 24, 2024
  1

• Plotting Error in basenji_test.py

  calico/basenji#203 · Filter by author ratheraarif opened on Dec 9, 2024
  2

• Using the same architecture and training parameters in pytorch, the model fails to converge.

  calico/basenji#201 · Filter by author bioczsun opened on Oct 31, 2024
  5

• akita train error

  calico/basenji#200 · Filter by author guandailu opened on Jul 31, 2024

• AssertionError, Basenji_test.py 'Conv1D' object has no attribute 'input_shape'

  calico/basenji#199 · Filter by author PouriaAzadehR opened on Jun 5, 2024
  5

• Question of expected data

  calico/basenji#198 · Filter by author seraphimangel77 opened on Jun 3, 2024
  1

• basenji_read overflow

  calico/basenji#196 · Filter by author ElArquitectorgo opened on May 20, 2024
  1

• Question about the preprocessing script bam_cov.py

  calico/basenji#195 · Filter by author Wenhui-bio opened on May 15, 2024
  1

• Problems during model training.

  calico/basenji#192 · Filter by author amingc3 opened on Apr 6, 2024
  8

• Reproduce the Enformer's input sequences split

  calico/basenji#190 · Filter by author sararb opened on Mar 5, 2024
  1

• Issue with final matrix?

  calico/basenji#188 · Filter by author 16nbb1 opened on Jan 11, 2024
  1

• When using Akita for single-cell prediction on the HCT116 cell line, the Pearson correlation coefficient is much lower.

  calico/basenji#186 · Filter by author TeaQAQTea opened on Nov 25, 2023
  8

• How to convert the keras model to a basenji model

  calico/basenji#180 · Filter by author houruiyan opened on Oct 9, 2023
  1

• Stable environment configuration

  calico/basenji#179 · Filter by author tzhu-bio opened on Sep 27, 2023
  1

• handling blacklist\unmappable

  calico/basenji#176 · Filter by author yardenmatok203 opened on Aug 21, 2023
  1

• Expose 'raw' as an argument?

  calico/basenji#173 · Filter by author Yaoyx opened on Aug 10, 2023
  2

• .hic

  calico/basenji#172 · Filter by author yardenmatok203 opened on Aug 6, 2023
  1