vaquerizaslab/chess

Issues

• chess extract error: operands could not be broadcast together with shapes

  #58 opened 5 months ago by zy041225
  1

• Deprecated parameters in scikit-image & scikit-learn

  #63 opened 9 months ago by niederhuth
  0

• Normalization of .hic files

  #62 opened a year ago by aminakur
  1

• Chess sim output .tsv file explained

  #61 opened a year ago by aminakur
  1

• data_range parameter not specified - error

  #59 opened a year ago by aminakur
  7

• _pickle.PicklingError

  #57 opened 2 years ago by PengfeiInTuebingen
  2

• speed up the chess run

  #51 opened 2 years ago by zy041225
  1

• something different from plotting

  #56 opened 2 years ago by ZQY19960810
  9

• error when running extract on .hic files

  #55 opened 2 years ago by ZQY19960810
  1

• error on running chess sim

  #54 opened 2 years ago by ZQY19960810
  2

• issue of normalized/chess extract

  #53 opened 2 years ago by ZQY19960810
  1

• error of the chess extract

  #52 opened 3 years ago by ZQY19960810
  3

• conservation analysis when only a few syntenic blocks are available

  #50 opened 3 years ago by zy041225
  3

• Prepare the normalized hic input for CHESS

  #35 opened 4 years ago by biozzq
  9

• Different resolution produce different result

  #48 opened 3 years ago by biozzq
  1

• Should the users be concerned about the problem raised in the new Contradictory Results bioRxiv preprint?

  #49 opened 3 years ago by P-GB-W
  2

• Conditions for conservation analysis of syntenic blocks

  #45 opened 3 years ago by luciaalvarez95
  5

• Get observed/expected from Juicer Hi-C

  #39 opened 4 years ago by sshen82
  2

• No valid region pairs found?

  #47 opened 3 years ago by gdolsten
  1

• It's difficult to find any significant changes in 3D organization of chromatin in highly dissimilar regions

  #34 opened 4 years ago by biozzq
  14

• Nan Continued

  #46 opened 3 years ago by drlaurenwasson
  2

• CNV bias in normalization

  #44 opened 4 years ago by jazberna1
  2

• chess --version doesn't work?

  #41 opened 4 years ago by liz-is
  0

• BEDPE file format

  #37 opened 4 years ago by ysora
  3

• Error when running CHESS on JUICER HIC files

  #38 opened 4 years ago by rkuzya
  2

• No valid pairs found problem

  #36 opened 4 years ago by sshen82
  5

• BED / BEDPE file handling - BEDPE file produced by `chess pairs` is not 0-based

  #32 opened 4 years ago by liz-is
  3

• how to deal with biological replicate

  #31 opened 4 years ago by biozzq
  4

• how to get the actual positions of the highly dissimilar regions highlighted by chess extract

  #29 opened 4 years ago by biozzq
  4

• non

  #14 opened 4 years ago by BenxiaHu
  2

• non

  #17 opened 4 years ago by BenxiaHu
  1

• Could not compute similarity for...

  #30 opened 4 years ago by liz-is
  4

• questions about the results of chess extract

  #28 opened 4 years ago by biozzq
  8

• plot output?

  #24 opened 4 years ago by rikrdo89
  1

• chess filter Unrecognized command

  #27 opened 4 years ago by biozzq
  2

• How to define the high confidence set of regions showing clear changes?

  #26 opened 4 years ago by biozzq
  2

• The example hic file cannot be dumped

  #21 opened 4 years ago by biozzq
  4

• Error when run chess_extract

  #25 opened 4 years ago by yanchunzhang
  3

• Chess sim quits with ERROR "all regions need to span at least 20 bins "

  #23 opened 4 years ago by rikrdo89
  16

• chess sim result wit all NAN

  #16 opened 4 years ago by chenggang108
  13

• Chess sim command runtime improvement heuristics?

  #18 opened 4 years ago by jmcbroome
  6

• Extracting genomic coordinates of differential features

  #10 opened 4 years ago by cgirardot
  17

• non

  #22 opened 4 years ago by BenxiaHu
  0

• non

  #13 opened 4 years ago by BenxiaHu
  3

• non

  #15 opened 4 years ago by BenxiaHu
  1

• Run time of chess sim module

  #20 opened 4 years ago by magnitov
  7

• Error while running "example analysis"

  #19 opened 4 years ago by Gonysh
  2

• The input image seems to have just one color 0.

  #12 opened 4 years ago by Evianyiyun
  4

• NaN continued

  #9 opened 4 years ago by cgirardot
  2

• hints to chess extract

  #11 opened 4 years ago by cgirardot
  1