Issues

• Usage with Docker

  ay-lab/FitHiChIP#112 · Filter by author roddypr opened on Mar 17, 2026
  7

• bedToBigBed version for FitHiChIP

  ay-lab/FitHiChIP#111 · Filter by author xiasijian opened on Jun 5, 2025

• Can exactTest be safely replaced with glmQLFit to add batch effect correction?

  ay-lab/FitHiChIP#110 · Filter by author EASS132 opened on Apr 20, 2025

• I met an error when computing ICE based bias vector from the HiC-pro contact matrix

  ay-lab/FitHiChIP#109 · Filter by author wingeredge opened on Apr 12, 2025

• Could FitHiChIP merge loops between different biological replicates?

  ay-lab/FitHiChIP#108 · Filter by author ZhangZhaoheng24 opened on Mar 18, 2025
  1

• cat: /volumes/easystore/HiChIP_CTCF/Matrix_BinSize5000/sample.interactions.initial.bed: No such file or directory - FitHiChIP is quiting

  ay-lab/FitHiChIP#107 · Filter by author hd931 opened on Jul 23, 2024
  1

• FitHiChIP_Singularity.sh ERROR

  ay-lab/FitHiChIP#106 · Filter by author yxralba088 opened on Jun 12, 2024

• Differential loop analysis

  ay-lab/FitHiChIP#105 · Filter by author helenhuangmath opened on Feb 29, 2024
  1

• FitHiChIP requests different input than specified in documentation

  ay-lab/FitHiChIP#104 · Filter by author roniweiss12 opened on Feb 4, 2024
  1

• An easy way to get the whole genome expected interaction matrix

  ay-lab/FitHiChIP#103 · Filter by author zhangylab opened on Dec 18, 2023
  1

• Error in .compressOffsets(y, offset = offset) : offsets must be finite values Calls: ApplyEdgeR -> exactTest -> mglmOneGroup -> .compressOffsets

  ay-lab/FitHiChIP#102 · Filter by author Gemma-Zhang-326 opened on Nov 17, 2023
  1

• How to get common loops between two samples

  ay-lab/FitHiChIP#101 · Filter by author ChaitaliChakraborty opened on Nov 8, 2023
  4

• option to fragment interactions?

  ay-lab/FitHiChIP#100 · Filter by author hugch2020 opened on Nov 1, 2023
  1

• Lower number of Significant Interactions

  ay-lab/FitHiChIP#98 · Filter by author koushik20 opened on Sep 14, 2023
  1

• mcool format as an input

  ay-lab/FitHiChIP#96 · Filter by author MariaMetelova opened on May 11, 2023
  1

• Error while using FitHiChIP_Docker.sh - Docker Image might be outdated

  ay-lab/FitHiChIP#94 · Filter by author dvesposito opened on Apr 26, 2023
  1

• Error in smooth.spline

  ay-lab/FitHiChIP#93 · Filter by author evaham1 opened on Apr 19, 2023
  1

• Running FitHiChIP error for .hic data

  ay-lab/FitHiChIP#91 · Filter by author cauyrd opened on Feb 17, 2023
  2

• fitHiChIP produces very small amount of peaks for H3K4me3 and H3K27ac

  ay-lab/FitHiChIP#89 · Filter by author FALab500 opened on Dec 22, 2022
  1

• Optional parameter to disable checking for HiCPro

  ay-lab/FitHiChIP#88 · Filter by author jeremyd85 opened on Nov 18, 2022
  3

• Unable to handle library error

  ay-lab/FitHiChIP#85 · Filter by author nahmed125 opened on Oct 18, 2022
  7

• Normalized contact value?

  ay-lab/FitHiChIP#80 · Filter by author yanchunzhang opened on Jul 13, 2022
  7

• ChIPSeqAlign file for differential analysis

  ay-lab/FitHiChIP#71 · Filter by author xumai-du opened on Jan 23, 2022
  9

• virtual 4C maps from FitHiChIP output

  ay-lab/FitHiChIP#3 · Filter by author gouthamatla opened on Dec 27, 2018