open2c/coolpuppy

Issues

• [BUG]matplotlib 3.9 broken dependency

  #160 opened a month ago by ljw20180420
  1

• Issue with Bed vs Bedpe feature format

  #158 opened 2 months ago by LucasMcNU
  3

• [Q] Access pileup matrix generated from coolpup.py

  #159 opened 2 months ago by LucasMcNU
  1

• [Q] Centromere Trans Pileup

  #157 opened 2 months ago by LucasMcNU
  2

• TypeError: unsupported operand type(s) for +: 'int' and 'str'

  #155 opened 3 months ago by ratheraarif
  5

• [Q]Understanding rescaling

  #152 opened 4 months ago by zhaoyycrow
  2

• [BUG]Labels messed up in plot_stripes lineplot=Treu

  #153 opened 5 months ago by zhaoyycrow
  2

• A large number of NAs ​​appear on the diagonal[Q]

  #156 opened 5 months ago by G1298192734a
  1

• Pileup for telomeres concerning trans chromosomal interactions

  #150 opened 7 months ago by Brahmandam-Gayatri
  26

• No chromosomes are in common between the coordinate file and the cooler file.

  #151 opened 6 months ago by ratheraarif
  9

• [Q]loop analysis takes long time

  #149 opened 7 months ago by jiangshan529
  6

• [BUG]Import error `from coolpuppy import plotpup`

  #147 opened 7 months ago by zhaoyycrow
  2

• [Q] How to test significance of change between pileups?

  #148 opened 7 months ago by AudreyBaguette
  1

• `pu.pileupsWithControl` might skip some pile-up regions or raise vague `domain_score not in dict2` AssertionError

  #146 opened 7 months ago by nvaulin
  1

• [Q] Setting --mindist parameter as 0, but not contain all number of loop(input loop.bedpe)

  #145 opened 8 months ago by Miracle-Yao
  3

• To access a value by position, use `ser.iloc[pos]` chroffset = self.clr.offset(region[0])

  #144 opened 8 months ago by jiangshan529
  2

• Extracting locus strength scores for loops

  #143 opened 9 months ago by NMaziak
  3

• ValueError: operands could not be broadcast together with shapes (125,125) (127,127)

  #135 opened 9 months ago by NMaziak
  4

• Y-Axis labels missing with plotpup.plot

  #142 opened 9 months ago by linus3210
  1

• [Q]How to get the matrix data after running coolpup.py

  #141 opened 10 months ago by valderpan
  3

• dividepups.py error

  #140 opened a year ago by BenxiaHu
  2

• [Q] Question on normalization between 2 conditions before coolpups

  #139 opened a year ago by Lucas446
  0

• Can coolpuppy use raw cool file to perform analysis?

  #138 opened a year ago by JiaoLaboratory
  4

• how to generate a my_hic_data_expected.tsv ?

  #137 opened a year ago by JiaoLaboratory
  0

• how to generate the expected.tsv?[Q]

  #136 opened a year ago by JiaoLaboratory
  1

• [Q]ValueError: Too few columns

  #134 opened a year ago by jiangshan529
  2

• [Q]Why is Pile-ups of interactions between a set of regions is so time cosuming?

  #132 opened a year ago by jiangshan529
  21

• [Q]Error in Apa

  #123 opened a year ago by ag-abhishek
  2

• Load/reoder chromosomes

  #131 opened a year ago by odovgusha
  1

• [Q] How to calculate the significance of clustering difference between to comparison groups?

  #117 opened a year ago by YuboWang1994
  2

• About plotpup.py error

  #133 opened a year ago by DontCareYaYa
  5

• [Q]only two huge squares in the final plot

  #120 opened 2 years ago by jiangshan529
  3

• [Q]why is the middle value not in the center of the color bar

  #121 opened 2 years ago by jiangshan529
  9

• cooltools pileup for CTCF and RAD21

  #125 opened 2 years ago by odovgusha
  6

• [Q]question about normalization

  #122 opened 2 years ago by jiangshan529
  3

• providing an array as argument for by_distance

  #129 opened 2 years ago by hrahmanin
  2

• APA score

  #128 opened 2 years ago by BenxiaHu
  19

• Argument `expected_value_col` in PileUpper methods is ignored

  #126 opened 2 years ago by hisakatha
  0

• [Q]When the new version performs rescaling pileup analysis, there is a problem with the ignore_diags parameter

  #124 opened 2 years ago by WANGchuang715
  5

• how to plot short and long contact frequency

  #111 opened 2 years ago by BenxiaHu
  6

• [Q]why the value on heatmap is zero

  #119 opened 2 years ago by jiangshan529
  9

• How does rescale work?

  #115 opened 2 years ago by Qiuhai-Zeng
  2

• No chromosomes are in common

  #110 opened 2 years ago by Qiuhai-Zeng
  9

• [Q]installing problem

  #118 opened 2 years ago by jiangshan529
  7

• how to plot interchromosome interactions

  #113 opened 2 years ago by BenxiaHu
  2

• how to plot difference

  #102 opened 2 years ago by BenxiaHu
  6

• Install error: module 'coolpuppy.lib'

  #104 opened 2 years ago by OdysseyXD
  2

• Resolution compatibility between .cool file and .bedpe file for pile-ups of predefined regions pairs

  #107 opened 2 years ago by Soh-hyon
  1

• saddle plot score

  #106 opened 2 years ago by BenxiaHu
  1

• saddle plot

  #101 opened 2 years ago by BenxiaHu
  1