broadinstitute/PhylogicNDT

Issues

• Warnings with example data

  #58 opened 3 years ago by rpensch
  1

• Relative timing for subregion (chr3q13.33 instead of chr3q)

  #72 opened 2 months ago by oghzzang
  0

• SinglePatientTiming: get_arm_level_cn_events

  #55 opened 3 years ago by iS4i4S
  5

• how to understand the result of com.tsv

  #70 opened a year ago by Elizabeth237
  1

• Retrieve the segment info of CNVs from the output

  #65 opened a year ago by lichennan123
  2

• Is the CorrectBias module undefined?

  #62 opened 2 years ago by moshl
  1

• About SinglePatientTiming demo

  #67 opened a year ago by RetGiraffe11235
  2

• ABSOLUTE for CCF

  #29 opened 5 years ago by mkinnaman
  7

• input of SinglePatientTiming

  #69 opened a year ago by Elizabeth237
  2

• tuple index out of range

  #68 opened a year ago by kangdong318
  0

• ModuleNotFoundError: No module named 'Sample'

  #44 opened 4 years ago by vicentepp
  1

• Protein_Change and Variant_Classification are None

  #64 opened 2 years ago by lincj1994
  2

• PureCN implementation of ABSOLUTE as input for phylogicNDT

  #45 opened 4 years ago by naumenko-sa
  1

• Allele-specific copy number from PhylogicNDT or ABSOLUTE

  #53 opened 3 years ago by juberpatel
  2

• Docker build fails

  #63 opened 2 years ago by emsisson
  0

• specifying output folder for singularity

  #49 opened 4 years ago by SebastianHollizeck
  3

• ccf histogram calculation

  #10 opened 5 years ago by rbonneville
  12

• A minor issue in SinglePatientTiming

  #42 opened 2 years ago by shwong-tw
  0

• Bad clustering with combines 0 CCF and 1 CCF mutations

  #61 opened 2 years ago by SebastianHollizeck
  0

• Protein_change and Protein_Change are inconformity in different scripts.

  #60 opened 2 years ago by YingYa
  0

• More than one tree was generated in Phylogic Results

  #59 opened 3 years ago by angelacho0113
  0

• "IndexError: list index out of range" in plot_1d_clusters

  #50 opened 4 years ago by SebastianHollizeck
  2

• What citation should be used for PhylogicNDT?

  #56 opened 3 years ago by bknisbac
  0

• BuildTree & GrowthKinetics cannot use -i parameter

  #2 opened 5 years ago by Jonathanyu2014
  2

• `--order_by_timepoint` not working

  #54 opened 3 years ago by abenjak
  0

• CCF of child cluster greater than parents

  #52 opened 4 years ago by nadia35
  1

• cluster 1 with clust_ccf_mean equal 1 was the clonal cluster ?

  #51 opened 4 years ago by smm19900210
  1

• Min number of mutations in each cluster

  #39 opened 5 years ago by mksamur
  1

• buildtree not showing private mutations

  #47 opened 4 years ago by vicentepp
  0

• Running cluster step on hypermutated tumour mutations

  #46 opened 4 years ago by bkinnersley
  0

• out of bounds error when running SinglePatientTiming

  #21 opened 4 years ago by shwong-tw
  5

• Log output destination configurable?

  #40 opened 4 years ago by csmith-pact
  0

• docker permission denied each time

  #37 opened 5 years ago by xhy1219
  0

• Indels not added in after clustering

  #35 opened 5 years ago by aktewari
  0

• behavior parameter --impute

  #34 opened 5 years ago by shwong-tw
  0

• IndexError

  #9 opened 5 years ago by SebastianHollizeck
  7

• example PhylogicNDT/ExampleRuns/PhylogicNDT-Example.ipynb is broken

  #23 opened 5 years ago by judithabk6
  0

• Copy number file cannot be properly used by PhylogicNDT

  #15 opened 5 years ago by Jonathanyu2014
  0

• The result of ABSOLUTE v1.0.6 cannot be used

  #4 opened 5 years ago by Jonathanyu2014
  6

• Error: No module named emd

  #11 opened 5 years ago by abenjak
  1

• --impute crashes

  #8 opened 5 years ago by SebastianHollizeck
  0

• Cannot run with example data

  #5 opened 5 years ago by SebastianHollizeck
  4