Commits · 12017b703260c8f1316e7995b7e8d58ce68b5075 · VEBER Philippe / codepi

19 Mar, 2021 5 commits
- update wrt phylogenetics · 12017b70
  Philippe Veber authored Mar 17, 2021
  
  12017b70
- added tests from phylogenetics · 98192f3b
  Philippe Veber authored Mar 17, 2021
  
  98192f3b
- renamed tk/Note to tk/Mdnote · ebcd68e9
  Philippe Veber authored Mar 16, 2021
  
  ebcd68e9
- tk/Mutsel_simulator_cpg: fixed out of bound error for sequences of size 1 · f54038b7
  Philippe Veber authored Mar 15, 2021
  
  f54038b7
- tk/Mutsel_simulator_cpg: fixed context definition · 04acf267
  Philippe Veber authored Mar 15, 2021
```
context should not include information on a codon, since it is used to
compute a rate matrix between all codons.
```
  04acf267
16 Mar, 2021 2 commits
- TDG09 : faster matrix exponentiation (hopefully ?) · b4e42135
  Louis Duchemin authored Mar 16, 2021
  
  b4e42135
- Calibration + benchmark merge · de17b6b5
  Louis Duchemin authored Mar 16, 2021
  
  de17b6b5
15 Mar, 2021 2 commits
- Mutsel CpG simulator demo · 84ebb3e3
  Louis Duchemin authored Mar 15, 2021
  
  84ebb3e3
- Fixed mutsel_simulator_cpg.mli : signature mismatch · 983286d5
  Louis Duchemin authored Mar 15, 2021
  
  983286d5
12 Mar, 2021 4 commits
- Mutsel CpG : more efficient implementation for dinucleotide ratios · bcf35ad0
  Louis Duchemin authored Mar 12, 2021
  
  bcf35ad0
- Fixes overflow error in Mutsel CpG dinucleotide ratios computation · 424c4047
  Louis Duchemin authored Mar 12, 2021
  
  424c4047
- Mutsel CpG : Fixed error in dinucleotide ratios computation · 94b3e90f
  Louis Duchemin authored Mar 12, 2021
  
  94b3e90f
- tk/Mutsel_simulator_cpg: cosmetic changes to dinucleotide_ratios · a17d17a6
  Philippe Veber authored Mar 12, 2021
  
  a17d17a6
11 Mar, 2021 6 commits
- Adds dinucleotide ratio computation in Mutsel_simulator_cpg · 10553ec5
  Louis Duchemin authored Mar 11, 2021
  
  10553ec5
- Calibration : multinomial + TDG09 + LMM pal histograms under Mutsel · 21f5f943
  Louis Duchemin authored Mar 11, 2021
  
  21f5f943
- Mutsel CpG simulator: update make_param signature · 8092353c
  Louis Duchemin authored Mar 11, 2021
```
Also adds some convenience functions for flat and random params
```
  8092353c
- Mutsel simulator stationary distribution · e764974c
  Louis Duchemin authored Mar 11, 2021
  
  e764974c
- tk/Mutsel_simulator_cpg: cosmetic changes · 3d706ee4
  Philippe Veber authored Mar 11, 2021
  
  3d706ee4
- whitespacecommit · 6d715ccb
  Philippe Veber authored Mar 11, 2021
  
  6d715ccb
10 Mar, 2021 1 commit
- Mutsel CpG simulator with flat parameters · d33cb5a3
  Louis Duchemin authored Mar 10, 2021
  
  d33cb5a3
09 Mar, 2021 1 commit
- Mutsel simulator with CpG hypermutability · 7b9b98b8
  Louis Duchemin authored Mar 09, 2021
  
  7b9b98b8
04 Mar, 2021 3 commits
- app/lmm_benchmark: added inhouse tdg09 · 18a83e34
  Philippe Veber authored Mar 04, 2021
  
  18a83e34
- ocamlinit: updated · 0a6a31de
  Philippe Veber authored Mar 04, 2021
  
  0a6a31de
- notes/calibration: fixed slide presentation · c5c62614
  Philippe Veber authored Mar 04, 2021
  
  c5c62614
02 Mar, 2021 6 commits
- Code to generate methods calibration report · 745165b2
  Louis Duchemin authored Mar 02, 2021
  
  745165b2
- added orthomam phenotypes made by Bastien · 186a5191
  Philippe Veber authored Mar 02, 2021
  
  186a5191
- app/Lmm_benchmark: cleanup · 4d54b9af
  Philippe Veber authored Mar 02, 2021
  
  4d54b9af
- Utils: fixed make_prc_dataset · 63ab3739
  Philippe Veber authored Mar 02, 2021
  
  63ab3739
- Simulation_pipeline: fixed PR AUC calculation in Mutsel.benchmark · cc080f19
  Philippe Veber authored Mar 02, 2021
  
  cc080f19
- tk/Result_table: fixed header when creating tables · 4d3d17c9
  Philippe Veber authored Mar 02, 2021
  
  4d3d17c9
01 Mar, 2021 1 commit
- Rerconverge : rename wip.ml to rer_omm.ml + tidy up stdout · 1940c313
  Louis Duchemin authored Mar 01, 2021
  
  1940c313
26 Feb, 2021 2 commits
- RERconverge : using Rconsole module to extract results + syntax error fix · 3d8e32a1
  Louis Duchemin authored Feb 26, 2021
  
  3d8e32a1
- In-house LMM x Gemma : fixes not positive-definite matrix · c39f81c7
  Louis Duchemin authored Feb 26, 2021
  
  c39f81c7
25 Feb, 2021 2 commits
- In-house LMM x Gemma hybrid performance evaluation · 23f9cbc2
  Louis Duchemin authored Feb 25, 2021
  
  23f9cbc2
- RERconverge : compute results for each foreground clade specification · d15d6813
  Louis Duchemin authored Feb 25, 2021
  
  d15d6813
24 Feb, 2021 2 commits
- RERconverge : fix relative rates plot · b722c7d9
  Louis Duchemin authored Feb 24, 2021
  
  b722c7d9
- RERconverge : fix bistro templates in main script · c74ebba1
  Louis Duchemin authored Feb 24, 2021
  
  c74ebba1
15 Feb, 2021 1 commit
- improved multinomial_and_phylogeny note · bd526da0
  Philippe Veber authored Feb 15, 2021
  
  bd526da0
12 Feb, 2021 2 commits
- refactor notes as bistro scripts · faa43e4d
  Philippe Veber authored Feb 12, 2021
  
  faa43e4d
- tk: new Tree_croquis module · 98de5ae0
  Philippe Veber authored Feb 12, 2021
  
  98de5ae0