morrislab/pairtree

Issues

• Manta VCFs

  #48 opened 4 months ago by alexanderchang1
  3

• Pairtree generating nonexistent variant IDs, leading to KeyError

  #52 opened 5 months ago by cathy-y
  4

• Weird results: no branching, just series of clusters

  #12 opened 6 months ago by J-Moravec
  3

• Getting different tree solutions with different pairtree run.

  #51 opened 7 months ago by itigupta2429
  3

• Adding CN to VCF file

  #46 opened 8 months ago by ElizabethBorden
  3

• pairtree requires older version of numpy

  #40 opened 8 months ago by agorelick
  3

• error in the step "bash make.sh" during installation

  #50 opened 8 months ago by DeMagicscience
  1

• Error while running pairtree

  #49 opened 9 months ago by itigupta2429
  2

• Which mutations does "node0" have??

  #47 opened a year ago by oghzzang
  6

• Trees output full results

  #6 opened 4 years ago by underbais
  6

• Run removegarbage takes too much time?

  #45 opened a year ago by THT-sleepy
  1

• math behind var_read_prob and other questions

  #43 opened a year ago by THT-sleepy
  2

• calculating var_read_prob column?

  #3 opened 4 years ago by ahgillmo
  2

• Hi, Aaron!

  #44 opened a year ago by THT-sleepy
  0

• is pairtree not also using longitudinal data?

  #42 opened a year ago by sahuno
  2

• Cluster members

  #39 opened a year ago by OumaimaHamza
  1

• how to extract number of clones per sample in results?

  #41 opened a year ago by sahuno
  4

• New tag

  #38 opened 2 years ago by SamD28
  1

• Finding trunk and branch clusters from json files

  #35 opened 2 years ago by shaghayeghsoudi
  1

• ValueError when plotting the tree

  #36 opened 2 years ago by OumaimaHamza
  2

• Contiguous variant IDs enforced?

  #34 opened 2 years ago by sabackman
  1

• Compatibility with R/bioconductor fishplot package

  #33 opened 2 years ago by jsha129
  3

• numba need Numpy 1.21 or less

  #25 opened 2 years ago by healthcare-mikeli
  0

• Choosing pairtree parameters

  #18 opened 2 years ago by underbais
  0

• Error: 'module' object is not callable

  #7 opened 2 years ago by J-Moravec
  0

• ‘for’ loop initial declarations are only allowed in C99 mode

  #13 opened 2 years ago by karini925
  0

• var_read_prob column in the .ssm file

  #31 opened 2 years ago by pushpa-itagi
  1

• cannot open shared object file: No such file or directory

  #32 opened 2 years ago by jubayer98
  2

• Annotating data from multiple timepoints + multiple regions

  #27 opened 2 years ago by AnishSomani
  1

• Is there a way to overlay samples' ratio or frequency on the tree nodes?

  #23 opened 2 years ago by ba3lwi
  1

• Selecting a solution based on negative log-likelihood

  #24 opened 2 years ago by ahgillmo
  1

• Calculation of Shannon index

  #30 opened 2 years ago by ahgillmo
  1

• FloatingPointError: invalid value encountered in true_divide

  #14 opened 3 years ago by davidchen0420
  0

• Math behind var_read_prob

  #17 opened 3 years ago by underbais
  3

• decreasing the runtime for pairtree clustervars

  #22 opened 3 years ago by ahgillmo
  1

• clustervars: in_params_fn and out_params_fn are not documented

  #11 opened 3 years ago by J-Moravec
  0

• Please, document output

  #10 opened 3 years ago by J-Moravec
  0

• remove_high_vaf.py

  #19 opened 3 years ago by brucemoran
  2

• TypeError

  #4 opened 4 years ago by brucemoran
  7

• (document the input files)

  #2 opened 4 years ago by brucemoran
  3

• Error using example data

  #1 opened 4 years ago by hdetering
  4