YosefLab/Cassiopeia

Issues

• Segmentation fault in cas.pp.align_sequences

  #246 opened 2 months ago by peipp410
  0

• Fitness estimation not included on readthedocs

  #245 opened 2 months ago by colganwi
  0

• "Aborted (core dumped)" during the align step in cassiopeia-preprocess

  #243 opened 2 months ago by sk7944
  2

• Does Cassiopeia have the Function to directly get fitness score?

  #244 opened 3 months ago by tenlives
  9

• #cassiopeia.pl.plot_matplotlib() failed to add meta_data information

  #241 opened 5 months ago by jinyongfan
  2

• make test error

  #183 opened 2 years ago by ask-more-questions
  8

• Potential Bug in intBC extract

  #237 opened 7 months ago by jefferyUstc
  1

• ILPSolverError: Potential Graph could not be found with solver parameters.

  #239 opened 6 months ago by tenlives
  4

• Colors in `cassiopeia.pl.plot_matplotlib` not reproducible

  #230 opened 6 months ago by Marius1311
  7

• How to use Cassiopia to analyze bulk DNA sequencing data

  #236 opened 6 months ago by yuangh16
  1

• “Error” in function `error_correct_intbcs_to_whitelist`

  #234 opened 9 months ago by jefferyUstc
  0

• Computing tree likelihoods

  #231 opened a year ago by Marius1311
  0

• Parameter tuning for the hybrid solver

  #224 opened a year ago by Marius1311
  2

• how to display cutsite name in cas.pl.plot_matplotlib

  #222 opened a year ago by tenlives
  1

• Check whether the ILP Solver is using Gurobi

  #218 opened a year ago by Marius1311
  2

• Example `reorder_children` in plotting tutorial

  #219 opened a year ago by mattjones315
  0

• Calculate cell level plasticity score

  #210 opened a year ago by YushaLiu
  3

• Cassiopeia does not finish after a couple of days

  #204 opened a year ago by YushaLiu
  4

• ILP solver failing

  #213 opened a year ago by Marius1311
  2

• Neighbor-Joining algorithm using weighted Hamming distance

  #212 opened a year ago by YushaLiu
  2

• Refactor `solver` module

  #214 opened a year ago by mattjones315
  0

• How to speed up evolutionary coupling computation

  #209 opened a year ago by Marius1311
  4

• Regular scRNA-seq data as only input for Cassiopeia

  #206 opened a year ago by ioyarzun
  2

• Unable to read pickled files due to renaming of module?

  #203 opened a year ago by ekmolloy
  3

• Segmentation Fault in error_correct_cellbcs_to_whitelist

  #198 opened a year ago by syntonym
  5

• Show legend for colorstrip when using cassiopeia.pl.plot_matplotlib

  #200 opened a year ago by YushaLiu
  1

• Possible bug in `cas.pl.upload_and_export_itol`

  #193 opened a year ago by tzeitim
  6

• Failed Numbaization of Distance Function is Not Caught

  #179 opened 2 years ago by ivalexander13
  1

• results produced by ilp_solver

  #188 opened 2 years ago by ask-more-questions
  5

• How many intBCs are in the intbc_whitelist?

  #191 opened 2 years ago by lamyankin
  2

• Error in resolve_umi_sequence

  #174 opened 2 years ago by cnk113
  5

• issues about assign_lineage_groups() function

  #187 opened 2 years ago by AmoriLi
  0

• ERROR in align

  #186 opened 2 years ago by cxyzju
  1

• Converting FASTQs into an unmapped BAM: Index out of range

  #185 opened 2 years ago by george-butler
  3

• pip in Makefile

  #178 opened 3 years ago by svenmh
  1

• Triplets Correct and RF functions both mutate the underlying tree

  #173 opened 3 years ago by richardyz98
  0

• Installation instructions in readme

  #171 opened 3 years ago by adamgayoso
  1

• File names, import issues

  #172 opened 3 years ago by adamgayoso
  0

• Target site reference fasta in the Science article "Single-cell lineages reveal the rates, routes, and drivers of metastasis in cancer xenografts"

  #165 opened 3 years ago by gloriafight
  1

• Support character matrix colorstrips in plotting

  #160 opened 3 years ago by Lioscro
  0

• AttributeError calling cassiopeia.pp.align_sequences

  #144 opened 3 years ago by oligomyeggo
  5

• understanding the character matrix

  #157 opened 3 years ago by ShouWenWang
  4

• Implement Utilities from KP-Tracer MS

  #149 opened 3 years ago by mattjones315
  0

• Command line tools not found

  #155 opened 3 years ago by ShouWenWang
  3

• Missing ~/.itolconfig

  #156 opened 3 years ago by ShouWenWang
  6

• Cophenetic Distance

  #152 opened 3 years ago by mattjones315
  0

• Optional Priors Usage in Reconstruction

  #151 opened 3 years ago by mattjones315
  0

• Cleanup pandas operations in preprocessing pipeline

  #138 opened 3 years ago by Lioscro
  0

• Missing data

  #136 opened 3 years ago by oligomyeggo
  20

• Deal with empty target site alleles appropriately

  #139 opened 3 years ago by Lioscro
  1