Issues

• Update saddle_strength() to properly compute 0 extent

  open2c/cooltools#565 · Filter by author ieres-amgen opened on Mar 23, 2026

• rearrange fails if 'name' column is not present in provided view table

  open2c/cooltools#563 · Filter by author dmalzl opened on Nov 17, 2025
  2

• cooltools.expected_cis is not applicable to circular chromosomes

  open2c/cooltools#562 · Filter by author oganesson76 opened on Sep 15, 2025

• Problem with Saddle-analyses

  open2c/cooltools#561 · Filter by author phil622 opened on Sep 9, 2025
  1

• Pandas future warning

  open2c/cooltools#560 · Filter by author thomas-reimonn opened on Sep 8, 2025
  1

• Cooltools pileup slow with mixed chromosomes

  open2c/cooltools#555 · Filter by author bskubi opened on Jun 30, 2025
  5

• cooltools 0.7.1 'from matplotlib.cm import register_cmap' & 'from matplotlib.colormaps import register' import errors (solved by downgrading matplotlib)

  open2c/cooltools#549 · Filter by author guoyun-chen opened on Mar 19, 2025

• Neither from matplotlib.cm import register_cmap nor from matplotlib.colormaps import register works in cooltools 0.7.1 for supporting matplotlib 3.9

  open2c/cooltools#544 · Filter by author ljw20180420 opened on Dec 11, 2024
  6

• first diagonal NaNs for smoothed expected_cis

  open2c/cooltools#509 · Filter by author gfudenberg opened on Mar 11, 2024

• allow alternate reductions for aggregation across diagonals

  enhancement
  open2c/cooltools#507 · Filter by author gfudenberg opened on Mar 4, 2024

• synchronize CLI and API defaults for get_expected_cis smoothing & aggregation

  enhancement
  open2c/cooltools#506 · Filter by author gfudenberg opened on Mar 4, 2024

• migrate log-smoothing to mini-library

  enhancement
  open2c/cooltools#505 · Filter by author gfudenberg opened on Mar 4, 2024
  2

• insulation & edge effects: consider masking?

  question
  open2c/cooltools#503 · Filter by author gfudenberg opened on Feb 27, 2024

• snippers: order of "select" and "snip" matters, but should it

  open2c/cooltools#502 · Filter by author sergpolly opened on Feb 18, 2024

• pileup around centromeres

  open2c/cooltools#491 · Filter by author ratheraarif opened on Jan 28, 2024
  16

• Needs a "cool" logo

  open2c/cooltools#490 · Filter by author thomas-reimonn opened on Jan 28, 2024

• systematic treatment of floating point warnings from numpy

  open2c/cooltools#482 · Filter by author sergpolly opened on Jan 18, 2024

• Unable to install with poetry

  open2c/cooltools#467 · Filter by author thomas-reimonn opened on Nov 6, 2023
  5

• Issue with cooltools.api.snipping.pileup() compatibility with bioframe/core/construction.py", line 150

  question
  open2c/cooltools#462 · Filter by author haleybianchi opened on Oct 6, 2023
  5

• Downsampling and cis counts

  enhancement
  open2c/cooltools#458 · Filter by author ddepierre opened on Aug 7, 2023
  2

• snippers use different arithmetics than cooler for determining bins from coordinates

  bug
  open2c/cooltools#446 · Filter by author Phlya opened on May 31, 2023
  

• eigs_cis: input checking

  enhancement
  open2c/cooltools#428 · Filter by author gfudenberg opened on Mar 30, 2023
  2

• pileup: bed vs. bedpe inference

  enhancement
  open2c/cooltools#427 · Filter by author gfudenberg opened on Mar 30, 2023
  2

• cooltools stats CLI

  enhancement
  open2c/cooltools#415 · Filter by author agalitsyna opened on Feb 2, 2023
  1

• cooltools eigs-cis CLI output

  enhancement
  open2c/cooltools#394 · Filter by author gfudenberg opened on Oct 10, 2022
  1