ay-lab/FitHiChIP

Issues

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

  #107 opened 5 months ago by hd931
  0

• Is there a way to visualize the arcs plot in IGV?

  #62 opened 3 years ago by jiangshan529
  7

• FitHiChIP_Singularity.sh ERROR

  #106 opened 6 months ago by yxralba088
  0

• Running FitHiChIP error for .hic data

  #91 opened 2 years ago by cauyrd
  2

• Differential loop analysis

  #105 opened 10 months ago by helenhuangmath
  1

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

  #103 opened a year ago by zhangylab
  1

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

  #102 opened a year ago by Gemma-Zhang-326
  1

• FitHiChIP requests different input than specified in documentation

  #104 opened a year ago by roniweiss12
  1

• How to get common loops between two samples

  #101 opened a year ago by remeseirogrp
  4

• option to fragment interactions?

  #100 opened a year ago by hugch2020
  1

• Should input cool files be balanced/normalized?

  #99 opened a year ago by nyuhic
  2

• Normalization of regions with focal copy number amplification

  #97 opened a year ago by dmuliaditan
  2

• Lower number of Significant Interactions

  #98 opened a year ago by koushik20
  1

• HiC-Pro installation issue in FitHiChIP

  #95 opened a year ago by koushik20
  7

• Reference genome used for inferring peaks from HiChIP data

  #92 opened 2 years ago by koushik20
  3

• Unable to handle library error

  #85 opened 2 years ago by nahmed125
  7

• Error while using FitHiChIP_Docker.sh - Docker Image might be outdated

  #94 opened 2 years ago by dvesposito
  1

• Optional parameter to disable checking for HiCPro

  #88 opened 2 years ago by jeremyd85
  3

• Error in smooth.spline

  #93 opened 2 years ago by evaham1
  1

• mcool format as an input

  #96 opened 2 years ago by MariaMetelova
  1

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

  #89 opened 2 years ago by FALab500
  1

• z

  #90 opened 2 years ago by mctackett20
  0

• ChIPSeqAlign file for differential analysis

  #71 opened 3 years ago by xumai-du
  9

• Singularity

  #79 opened 2 years ago by pna059
  2

• /FitHiChIP/FitHiChIP_HiCPro.sh: line 841: [[: 0.01: syntax error: invalid arithmetic operator (error token is ".01")

  #82 opened 2 years ago by YichaoOU
  4

• Syntax error when using Docker for executing FitHiChIP

  #83 opened 2 years ago by Soh-hyon
  2

• error in evaluating the argument 'table' in selecting a method for function 'match': undefined columns selected

  #87 opened 2 years ago by Gemma-Zhang-326
  2

• Running FitHiChIP did not report any error, only print 'SORRY !!!!!!!! ……'

  #81 opened 2 years ago by Miracle-Yao
  5

• Files in EdgeR_Loops_* folder are all blank but title when running differential FitHiChIP analysis

  #86 opened 2 years ago by Gemma-Zhang-326
  1

• FitHiChIP compatibility with the dm6 Drosophila melanogaster genome.

  #84 opened 2 years ago by JosephAguilera
  5

• Normalized contact value?

  #80 opened 2 years ago by yanchunzhang
  7

• CHIP-seq inferred from HICHIP peak

  #69 opened 2 years ago by xumai-du
  1

• mcfork error while using TestData

  #59 opened 2 years ago by sillysean
  4

• Hicpro version

  #68 opened 2 years ago by xumai-du
  3

• check the version

  #77 opened 2 years ago by wbszhu
  2

• CombineNearbyInteraction failing

  #78 opened 2 years ago by pna059
  3

• Indexing of large genomes

  #74 opened 3 years ago by pna059
  1

• Number of locus pairs with nonzero contact count is zero - FitHiChIP is quiting !!!

  #75 opened 3 years ago by poflawless
  4

• Very small number of significant interactions

  #76 opened 3 years ago by arakawa7
  4

• Halts at Regression Model

  #70 opened 3 years ago by vivianschu
  5

• Error in hist.default(histdata$dist, breaks = seq(min_dist, max_dist, :

  #72 opened 3 years ago by hanshanmengqi
  3

• Use of `histdata$dist` is discouraged. Use `dist` instead.

  #73 opened 3 years ago by poflawless
  1

• curious about peak to all and peak to peak

  #63 opened 3 years ago by jiangshan529
  4

• how to do differential analysis for drug treated sample?

  #65 opened 3 years ago by jiangshan529
  1

• compare and rank loops

  #60 opened 3 years ago by wbszhu
  0

• is there any normalization step?

  #64 opened 3 years ago by jiangshan529
  2

• promoter capture Hi-C analysis

  #61 opened 3 years ago by BenxiaHu
  1

• More details about the example data

  #67 opened 3 years ago by zxwang2019
  2

• Differential Loop Analysis

  #66 opened 3 years ago by vivianschu
  4

• 'No child processes' in select, wrong formatted BED file and python3 error

  #54 opened 4 years ago by moritzschaefer
  3