Commits · c39f81c77a8028fa1eefbeff6958376660121192 · VEBER Philippe / codepi

26 Feb, 2021 1 commit
- 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 5 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
- Autoformat orthomam and RERconverge · b9ecba29
  Louis Duchemin authored Feb 12, 2021
  
  b9ecba29
- RERconverge : refactoring ; add relative rates plot · 714eb75d
  Louis Duchemin authored Feb 12, 2021
  
  714eb75d
- RER converge : refactor R scripts to save RDS file · bbfc9c93
  Louis Duchemin authored Feb 12, 2021
  
  bbfc9c93
11 Feb, 2021 2 commits
- Orthomam: added search_alignments · bbefd69d
  Philippe Veber authored Feb 11, 2021
  
  bbefd69d
- 'someone' commited without compiling · 5a0ce9ae
  Philippe Veber authored Feb 11, 2021
  
  5a0ce9ae
08 Feb, 2021 3 commits
- Gemma : formatting with ocp-indent · 63e50619
  Louis Duchemin authored Feb 08, 2021
  
  63e50619
- LMM : formatting with ocp-indent · 84afc72a
  Louis Duchemin authored Feb 08, 2021
  
  84afc72a
- LMM * Gemma hybridation : use Gemma correlation matrix · 0bfae62a
  Louis Duchemin authored Feb 08, 2021
  
  0bfae62a
05 Feb, 2021 3 commits
- RERconverge : update launch script with more phenotypes · b4666958
  Louis Duchemin authored Feb 05, 2021
  
  b4666958
- Orthomam.Binary_phenotype : module to load binary phenotypes annotations · 9b141cd6
  Louis Duchemin authored Feb 05, 2021
  
  9b141cd6
- RERconverge : fix gene ids in candidate summary · 0bb66ae6
  Louis Duchemin authored Feb 05, 2021
  
  0bb66ae6
02 Feb, 2021 2 commits
- RERconverge : enrichment analysis script · a11e5a1f
  Louis Duchemin authored Feb 02, 2021
  
  a11e5a1f
- RERconverge pipeline : working results summary · 346dfbcf
  Louis Duchemin authored Feb 02, 2021
  
  346dfbcf
28 Jan, 2021 1 commit
- RERconverge : candidate sites summary · 659364c9
  Louis Duchemin authored Jan 28, 2021
  
  659364c9
22 Jan, 2021 1 commit
- RERconverge : last fixes, enabling full run without errors · 23cb6047
  Louis Duchemin authored Jan 22, 2021
  
  23cb6047
21 Jan, 2021 3 commits
- rer_converge: fixes on script · 30614834
  Philippe Veber authored Jan 21, 2021
  
  30614834
- RERconverge : Rearrangement of gene trees to match species tree · 073aba01
  Louis Duchemin authored Jan 21, 2021
  
  073aba01
- RERconverge: don't use master_tree and add keep_ident to iqtree invocation · 5e8aa074
  Philippe Veber authored Jan 21, 2021
  
  5e8aa074
18 Jan, 2021 1 commit
- more fixes for rer converge, still not working though · 30b9a1dd
  Philippe Veber authored Jan 18, 2021
  
  30b9a1dd
15 Jan, 2021 9 commits
- RERconverge executable (wip) · 6d392a45
  Louis Duchemin authored Jan 15, 2021
  
  6d392a45
- Orthomam : adjusting pipeline upstream of rer_converge · 88297304
  Louis Duchemin authored Jan 15, 2021
  
  88297304
- Orthomam : add type annotations to clip_tree_on_alignment · 4a7cbafd
  Louis Duchemin authored Jan 15, 2021
  
  4a7cbafd
- Fixed typo in orthomam · cf04dbb7
  Louis Duchemin authored Jan 15, 2021
  
  cf04dbb7
- Setup docker for RER converge · 3a8f0be2
  Louis Duchemin authored Jan 15, 2021
  
  3a8f0be2
- Change Orthomam.rer_converge signature · f5ba4432
  Louis Duchemin authored Jan 15, 2021
  
  f5ba4432
- RER converge start up handle from orthomam · 92bcfe14
  Louis Duchemin authored Jan 15, 2021
  
  92bcfe14
- RER converge autoformat · d79f5bbb
  Louis Duchemin authored Jan 15, 2021
  
  d79f5bbb
- RER converge : phenotypes file from species list · ccba87bb
  Louis Duchemin authored Jan 15, 2021
  
  ccba87bb
14 Jan, 2021 2 commits
- RER converge pipeline · 822dfab1
  Louis Duchemin authored Jan 14, 2021
  
  822dfab1
- Merge branch 'new-cli' · 12048c65
  Philippe Veber authored Jan 14, 2021
  
  12048c65
21 Dec, 2020 1 commit
- Run: added pcoc method · 6a7e6b9a
  Philippe Veber authored Dec 21, 2020
  
  6a7e6b9a
20 Dec, 2020 1 commit
- Run: command-line choice of methods · 9be15cf6
  Philippe Veber authored Dec 20, 2020
  
  9be15cf6