Issues

• findModules peaks at about 7 gene x gene matrices of memory (44 GB at 30,000 genes)

  mortazavilab/PyWGCNA#156 · Filter by author ChenHsieh opened on Oct 15, 2026

• Question about number of genes in the computed modules

  mortazavilab/PyWGCNA#154 · Filter by author rodriguezalba opened on Feb 26, 2026

• Support for parallelism/multi-threading

  mortazavilab/PyWGCNA#153 · Filter by author fantauzzi opened on Jan 11, 2026

• SVD for module eigen gene instead of PCA or eigendecomposition of a similarity matrix

  mortazavilab/PyWGCNA#152 · Filter by author DCalhas opened on Jan 8, 2026

• Coexpression Module Plot creates unpredictable plots when more than one module is passed

  mortazavilab/PyWGCNA#151 · Filter by author annaliesemeyer opened on Nov 7, 2025

• Error for the quick start tutorial, I use Python 3.13.7

  mortazavilab/PyWGCNA#150 · Filter by author yudalang3 opened on Nov 6, 2025

• cutreeHybrid fails when pamRespectsDendro=True with ValueError: operands could not be broadcast together with shapes

  mortazavilab/PyWGCNA#149 · Filter by author potulabe opened on Nov 5, 2025

• Formatting for time series data with two replicates?

  mortazavilab/PyWGCNA#146 · Filter by author serenalotreck opened on Jul 24, 2025

• 'NoneType' object has no attribute 'render' when using CoexpressionModulePlot

  mortazavilab/PyWGCNA#145 · Filter by author realzhipeng opened on Jul 22, 2025

• not possible to see gene significance value?

  mortazavilab/PyWGCNA#144 · Filter by author realzhipeng opened on Jul 22, 2025

• barplotModuleEigenGene() Error w/ Tutorial and Data - colorBar

  mortazavilab/PyWGCNA#143 · Filter by author park-minjun opened on Jul 8, 2025
  1

• Custom input distance matrix?

  mortazavilab/PyWGCNA#142 · Filter by author kmuench opened on May 20, 2025

• What is the default behavior for unassigned genes?

  mortazavilab/PyWGCNA#141 · Filter by author lorenzoamir opened on May 5, 2025

• AttributeError: Unable to plot module eigengenes

  mortazavilab/PyWGCNA#140 · Filter by author LornaWessels opened on Mar 7, 2025

• support analysis related to Cytoscape

  improvement
  Feature

  mortazavilab/PyWGCNA#134 · Filter by author MSaadfarooq opened on Jan 29, 2025
  2

• Modules Not Visible After Running findModules()

  mortazavilab/PyWGCNA#127 · Filter by author victorsanchezarevalo opened on Nov 16, 2024
  1

• preprocessing fail when 'show' is set to True

  mortazavilab/PyWGCNA#121 · Filter by author nponts opened on Oct 3, 2024
  1

• Some suggestions (multithreading capabilities and GPU integration)

  enhancement
  mortazavilab/PyWGCNA#118 · Filter by author HemlockPoison opened on Sep 17, 2024
  3

• Plot issue (Image size is too large)

  mortazavilab/PyWGCNA#115 · Filter by author nliorni opened on Aug 15, 2024
  2

• Several errors when performing findModules steps individually

  mortazavilab/PyWGCNA#97 · Filter by author ghost opened on May 7, 2024
  8

• calculate Gene Significance

  enhancement
  mortazavilab/PyWGCNA#72 · Filter by author bsb2014 opened on Oct 26, 2023
  8

• Error with function analyseWGCNA()

  improvement
  mortazavilab/PyWGCNA#48 · Filter by author GERMAN00VP opened on Jun 21, 2023
  3

• Error appearance in PyWGCNA (version 1.2.4) in Google colaboratory

  mortazavilab/PyWGCNA#46 · Filter by author YoshifumiMiyagi opened on Jun 20, 2023
  6

• x and y ticks

  enhancement
  mortazavilab/PyWGCNA#27 · Filter by author wangjiawen2013 opened on Apr 3, 2023 · add matplotlib options
  1

• Consensus Modules

  mortazavilab/PyWGCNA#6 · Filter by author nmank opened on Jun 27, 2022
  13