Issues

• Request to release the GPU-enabled version of Hotspot on PyPI

  YosefLab/Hotspot#59 · Filter by author OMIC-coding opened on Aug 13, 2026

• data size limitations?

  YosefLab/Hotspot#58 · Filter by author Aditya-Gautam20 opened on May 18, 2026

• Any suggestion about hotspot analysis on scATAC data

  YosefLab/Hotspot#55 · Filter by author LongpanICR opened on Jan 2, 2026

• R

  YosefLab/Hotspot#53 · Filter by author JWJ13164328557 opened on Nov 11, 2025

• plot like spottedpy

  YosefLab/Hotspot#51 · Filter by author worker000000 opened on Jun 25, 2025

• hs.create_modules is a random number seed set in this function, why do I run the same code every time the number of modules is not consistent

  YosefLab/Hotspot#46 · Filter by author ZhangZao-HB opened on Feb 24, 2025

• compute_local_correlations not stop

  YosefLab/Hotspot#44 · Filter by author solivehong opened on Dec 25, 2024

• Supporting the analysis of multi-sample SRT data

  YosefLab/Hotspot#43 · Filter by author Antidington opened on Dec 5, 2024
  6

• hs.module_scores return nothing

  YosefLab/Hotspot#42 · Filter by author lvmt opened on Nov 28, 2024

• Autocorrelations of subset of genes against all genes

  YosefLab/Hotspot#38 · Filter by author jnmark opened on May 24, 2024

• 10x visium data

  YosefLab/Hotspot#37 · Filter by author wangjiawen2013 opened on Mar 15, 2024

• Getting 5 times more gene in a module than min_gene_threshold

  YosefLab/Hotspot#36 · Filter by author amissarova opened on Feb 14, 2024
  1

• Image parameter description

  YosefLab/Hotspot#35 · Filter by author Zhenbin24 opened on Feb 4, 2024

• Question about scalability

  YosefLab/Hotspot#34 · Filter by author smorabit opened on Aug 9, 2023

• Running hotspot on integrated data

  YosefLab/Hotspot#32 · Filter by author bbergsneider opened on Apr 28, 2023
  3

• How to save a Hotspot object for spatial data?

  YosefLab/Hotspot#30 · Filter by author aaadc opened on Oct 11, 2022

• InvalidIndexError: (slice(None, None, None), (0, 1)) when using sc.pl.spatial

  YosefLab/Hotspot#29 · Filter by author Flyingcattle opened on Jul 25, 2022
  3

• ValueError

  YosefLab/Hotspot#27 · Filter by author tongjiezhao opened on Jul 1, 2022
  6

• Run Hotspot without umi-count normalization

  YosefLab/Hotspot#25 · Filter by author TangLabsysu2020 opened on Jun 1, 2022

• create_modules speed up

  YosefLab/Hotspot#24 · Filter by author wangjiawen2013 opened on May 30, 2022
  4

• Question about phylogenetic tree type

  YosefLab/Hotspot#11 · Filter by author liangzhenhou opened on Dec 21, 2021

• Return figure in plot_local_correlations

  enhancement
  YosefLab/Hotspot#8 · Filter by author deto opened on Jul 6, 2021