Issues

• Model that some leaves might be doublets/cycling?

  UBC-Stat-ML/nowellpack#48 · Filter by author alexandrebouchard opened on Sep 11, 2019

• Run with various bin sizes: do larger bins kill the inference

  UBC-Stat-ML/nowellpack#46 · Filter by author alexandrebouchard opened on Nov 23, 2018

• Forward simulators: ABC?

  UBC-Stat-ML/nowellpack#45 · Filter by author alexandrebouchard opened on Nov 23, 2018

• Use discordant reads as input data?

  UBC-Stat-ML/nowellpack#44 · Filter by author alexandrebouchard opened on Oct 10, 2018
  2

• Small tasks

  humi
  UBC-Stat-ML/nowellpack#43 · Filter by author alexandrebouchard opened on Oct 10, 2018

• Indicators of target failure

  humi
  UBC-Stat-ML/nowellpack#42 · Filter by author alexandrebouchard opened on Oct 10, 2018

• Use initial population information

  humi
  UBC-Stat-ML/nowellpack#41 · Filter by author alexandrebouchard opened on Oct 10, 2018

• Validation based on point mutations

  UBC-Stat-ML/nowellpack#40 · Filter by author alexandrebouchard opened on Aug 29, 2018

• Validation based on classical characters? E.g. morphological traits?

  UBC-Stat-ML/nowellpack#38 · Filter by author alexandrebouchard opened on Aug 29, 2018

• Update the pipeline

  UBC-Stat-ML/nowellpack#37 · Filter by author alexandrebouchard opened on Aug 29, 2018

• Look at frequency spectrum statistics of trees to assess selection signal

  UBC-Stat-ML/nowellpack#36 · Filter by author alexandrebouchard opened on Aug 29, 2018
  2

• Pairing of events

  UBC-Stat-ML/nowellpack#35 · Filter by author alexandrebouchard opened on Aug 27, 2018

• Detection and mitigation of compound bins

  UBC-Stat-ML/nowellpack#34 · Filter by author alexandrebouchard opened on Aug 27, 2018

• Sanity check validation by in silico mixing

  UBC-Stat-ML/nowellpack#33 · Filter by author alexandrebouchard opened on Aug 27, 2018
  1

• Fix data conventions

  UBC-Stat-ML/nowellpack#32 · Filter by author alexandrebouchard opened on Aug 19, 2018

• Investigate prior sensitivity

  UBC-Stat-ML/nowellpack#31 · Filter by author alexandrebouchard opened on Aug 18, 2018

• Update instructions - they are outdated

  UBC-Stat-ML/nowellpack#28 · Filter by author alexandrebouchard opened on Aug 18, 2018

• Running on merged clones of OV2295, OV2295(R2), TOV2295(R) cell lines

  UBC-Stat-ML/nowellpack#25 · Filter by author alexandrebouchard opened on Aug 18, 2018
  1

• Running on 9k cells as a scalability demonstration

  UBC-Stat-ML/nowellpack#24 · Filter by author alexandrebouchard opened on Aug 18, 2018

• Run on SA 501 - check if X-loss occurs in a clade as validation

  UBC-Stat-ML/nowellpack#23 · Filter by author alexandrebouchard opened on Aug 18, 2018

• Compatibility with 10X CNV output

  enhancement
  UBC-Stat-ML/nowellpack#22 · Filter by author kieranrcampbell opened on Aug 8, 2018
  5

• Transition probabilities from HMMcopy

  UBC-Stat-ML/nowellpack#20 · Filter by author kieranrcampbell opened on Jul 30, 2018
  1

• Use Divide-and-Conquer SMC to impute branch lengths

  UBC-Stat-ML/nowellpack#18 · Filter by author alexandrebouchard opened on Jul 29, 2018

• Migrate generation process mechanism to explicit false positive/false negative

  UBC-Stat-ML/nowellpack#15 · Filter by author alexandrebouchard opened on Jul 28, 2018
  1