deeptools/HiCExplorer

Issues

• ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()

  #910 opened 3 months ago by mw18f
  0

• deprecated alias `np.float` from numpy when run hicDetectLoops to call loops

  #908 opened 3 months ago by joey0214
  1

• Fastq polishing

  #909 opened 3 months ago by DakeshiKitano
  1

• hicPCA error: IndexError: list index out of range. raise ValueError('`x` and `y` must have length at least 2.') ValueError: `x` and `y` must have length at least 2.

  #907 opened 5 months ago by shRDJr
  0

• About hicPCA error

  #898 opened 9 months ago by HW-Superior
  1

• hicMergeMatrixBins changes chromosome sizes

  #906 opened 6 months ago by qolba
  2

• No module named 'hic2cool'

  #903 opened 6 months ago by sanjin725
  1

• Clarification on Matrix Preprocessing for hicDifferentialTAD

  #905 opened 6 months ago by GuanrongYan
  0

• Misleading Documentation for --tadDomains, -td Parameter in hicDifferentialTAD Tool

  #904 opened 6 months ago by GuanrongYan
  0

• hicPCA " invalid literal" error message

  #883 opened a year ago by erbon7
  2

• HiC merging bins

  #900 opened 8 months ago by kunaltin2012
  0

• Question about sorting bam files

  #879 opened 9 months ago by Naveen-Ahuja
  4

• hicTrainTADClassifier raises ValueError

  #890 opened a year ago by bgruening
  1

• error in running hicDetectLoops

  #899 opened 9 months ago by pangulu
  0

• hicPCA -we default option

  #867 opened a year ago by StrohD
  2

• Can I use hicDifferentialTAD to analyze the TAD differences among three samples?

  #897 opened 9 months ago by ZJU-Plumber
  0

• hicFindTADs difficult to distinguish different TADs

  #896 opened 10 months ago by wangguiqian
  3

• hicCorrectMatrix correct

  #895 opened 10 months ago by wangguiqian
  0

• hicPCA flip signs with rna-seq?

  #892 opened a year ago by Naveen-Ahuja
  1

• hicMergeLoops throws an error

  #889 opened 10 months ago by portbo
  1

• problem with hicAggragateContacts

  #894 opened 10 months ago by eferreA9
  0

• installation failure :: trained_models missing from requirements

  #893 opened a year ago by EricDeveaud
  0

• LearningWithNoisyLabels was renamed to

  #891 opened a year ago by bgruening
  0

• Abound hicexplorer tools

  #857 opened a year ago by GleeenSIBS
  1

• hicBuildMatrix TypeError

  #888 opened a year ago by Claudiolete
  1

• problem with chicViewpoint

  #887 opened a year ago by robin-sto
  1

• how to plot a hic matrix starting from a .hic file?

  #886 opened a year ago by AlcaArctica
  3

• chicViewpointBackgroundModel and `np.int` aliases deprecated in NumPy 1.20

  #877 opened a year ago by amv33576
  7

• hicCompareMatrices between 2 cool format files

  #882 opened a year ago by BenxiaHu
  3

• --genome not working

  #885 opened a year ago by robertferr
  1

• HiCExplorer 3.5.2

  #884 opened a year ago by robin-sto
  2

• hicBuildMatrix hicCorrectMatrix ValueError: Axis limits cannot be NaN or Inf

  #881 opened a year ago by lkiko
  0

• chicViewpoint hangs indefinitely when reference file is a BED file with (non-unique) gene names in 4th column

  #880 opened a year ago by mtekman
  0

• 'Styler' object has no attribute 'render'

  #862 opened a year ago by pillailab
  3

• AttributeError: module 'cooler' has no attribute 'io'

  #871 opened a year ago by vakh57
  3

• Installation with newer version of `matplotlib`: "`ValueError: Passing a Normalize instance simultaneously with vmin/vmax is not supported.`"

  #873 opened a year ago by kalavattam
  1

• chicQualityControl fails with ImportError (conda version 3.7.2)

  #876 opened a year ago by mtekman
  2

• isuue with mcool to hic

  #866 opened a year ago by zzhoujialu
  2

• hicDetectLoops 'neihgborhood_unsmoothed' is not defined

  #860 opened 2 years ago by Matheo-LESNE
  1

• conda/mamba installation not working with python=3.11

  #864 opened a year ago by aminakur
  3

• Installation issue.

  #870 opened a year ago by ratheraarif
  1

• There is no data for the region considered on the matrix.

  #872 opened a year ago by ec233133
  7

• hicNormalize Behavior of operations on cool file

  #869 opened a year ago by rysterzhu
  1

• hicPlotMatrix "--region 1:10000000-50000000" option is abnormal

  #868 opened a year ago by JiaoLaboratory
  1

• conda install problem

  #861 opened 2 years ago by jiangshan529
  1

• hicPCA error

  #858 opened a year ago by MurliNair
  5

• ValueError: not enough values to unpack (expected 3, got 0)

  #865 opened a year ago by guo-cheng
  0

• hicDifferentialTAD TypeError

  #863 opened a year ago by CriticalSci
  1

• hicPlotMatrix to make one heatmap plot for two conditions

  #859 opened 2 years ago by liufuyan2016
  0

• --setToZeroThreshold 1.0 for normalization method smallest

  #856 opened 2 years ago by MWSchmid
  0