Commits · 5649b154c49ea6eb57880ac18c67e6706604a801 · VEBER Philippe / codepi · GitLab

31 Jul, 2018 6 commits
- add analyses_night · 5649b154
  Carine Rey authored Jul 31, 2018
  
  5649b154
- new test tree · 1983273e
  Carine Rey authored Jul 31, 2018
  
  1983273e
- use recall/precision to choose the threshold + new hypothesis (bigNeinSmallNe and SmallNeInBigNe) · a46650d4
  Carine Rey authored Jul 31, 2018
  
  a46650d4
- fix error with HaPC*Ne · 3d0b2086
  Carine Rey authored Jul 31, 2018
  
  3d0b2086
- use predefined pairs of profiles in function of their distance · 5fc3531f
  Carine Rey authored Jul 31, 2018
  
  5fc3531f
- add phyml to re infer tree after simu · f22a7cf1
  Carine Rey authored Jul 31, 2018
  
  f22a7cf1
27 Jul, 2018 2 commits
- Corrected bug when pair bins contain only 1 value. · 5ea6131a
  LANORE Vincent authored Jul 27, 2018
  
  5ea6131a
- Changed generate_pairs to output a table of pair indices instead of raw profiles + fixed sorting · a2c8e384
  LANORE Vincent authored Jul 27, 2018
  
  a2c8e384
26 Jul, 2018 7 commits
- generate_pairs: added toggle for distance type. · f84c8737
  LANORE Vincent authored Jul 26, 2018
  
  f84c8737
- generate_pairs: added debug + changed default bin bounds + added png output · 76a56a0b
  LANORE Vincent authored Jul 26, 2018
  
  76a56a0b
- Improved bin size in distance distribution plot. · 8ef90930
  LANORE Vincent authored Jul 26, 2018
  
  8ef90930
- Added option to display plot of pair distributions. · 526093fe
  LANORE Vincent authored Jul 26, 2018
  
  526093fe
- Added an option to specify number of pairs per distance class. · f46a8534
  LANORE Vincent authored Jul 26, 2018
  
  f46a8534
- New bin logic now properly works :) · 5cb204b1
  LANORE Vincent authored Jul 26, 2018
  
  5cb204b1
- Added bin specification in generate_pairs command line (not yet implemented) · 31565450
  LANORE Vincent authored Jul 26, 2018
  
  31565450
25 Jul, 2018 9 commits
- remove header · 2c31730e
  Carine Rey authored Jul 25, 2018
  
  2c31730e
- add type profile + split profile_fn in 3 classes at the beginning of the pipeline · 2a8d34e1
  Carine Rey authored Jul 25, 2018
  
  2a8d34e1
- add matplotlib and docopt in python docker · 525b1d4f
  Carine Rey authored Jul 25, 2018
  
  525b1d4f
- generate_pairs now outputs separate files for distance classes (separation... · 0067c5c2
  LANORE Vincent authored Jul 25, 2018
```
generate_pairs now outputs separate files for distance classes (separation into classes is very simple so far :/)
```
  0067c5c2
- Added Jensen-Shannon divergence and distance + added progress bar · 2ec82128
  LANORE Vincent authored Jul 25, 2018
  
  2ec82128
- generate_pairs now outputs a tsv of profile pairs + distance · b255b6ba
  LANORE Vincent authored Jul 25, 2018
  
  b255b6ba
- More work towards generate_pairs. Now able to pick profiles and compute... · 4f6531ee
  LANORE Vincent authored Jul 25, 2018
```
More work towards generate_pairs. Now able to pick profiles and compute euclidian distance between them.
```
  4f6531ee
- Changed 263 profiles from ssv to tsv · f4d28bc5
  LANORE Vincent authored Jul 25, 2018
  
  f4d28bc5
- Started working on generate_pairs.py script to generate sorted profile pairs. · 3e25eb7a
  LANORE Vincent authored Jul 25, 2018
  
  3e25eb7a
24 Jul, 2018 2 commits
- keep running infos · 172cee79
  Carine Rey authored Jul 24, 2018
  
  172cee79
- autoincremente the number of diffsel iterations · 3d7a93df
  Carine Rey authored Jul 24, 2018
  
  3d7a93df
23 Jul, 2018 7 commits
- fixed scripts/plot_sens_spe_all_trees · 6435d849
  Philippe Veber authored Jul 23, 2018
  
  6435d849
- add msd_meth (not working well yet due to output msd format but compile) · 8f3a909f
  Carine Rey authored Jul 23, 2018
  
  8f3a909f
- Corrections to msd files and makefile so it compiles. Msd dockerfile now works. · 6ae4542d
  LANORE Vincent authored Jul 23, 2018
  
  6ae4542d
- Updated diffsel docker + improved Dockerfile so it doesn't cache git clone +... · b43d2d28
  LANORE Vincent authored Jul 23, 2018
```
Updated diffsel docker + improved Dockerfile so it doesn't cache git clone + changed image name in pipeline.
```
  b43d2d28
- update r_basics docker version (add pandoc) · 8a17aa45
  Carine Rey authored Jul 23, 2018
  
  8a17aa45
- add final convergence checking of diffsel · f10560c8
  Carine Rey authored Jul 23, 2018
  
  f10560c8
- try to compile msd (not working) · 9696a2ad
  Carine Rey authored Jul 23, 2018
  
  9696a2ad
20 Jul, 2018 7 commits
- typoq · ca7b4eaa
  Carine Rey authored Jul 20, 2018
  
  ca7b4eaa
- add an option to run test hyp · 0e8ab97f
  Carine Rey authored Jul 20, 2018
  
  0e8ab97f
- get more info from simus · 10badf91
  Carine Rey authored Jul 20, 2018
  
  10badf91
- add 2 hypothesis based on different Ne, H0_BigNeInSmallNe and H0_SmallNeInBigNe · e51ad99e
  Carine Rey authored Jul 20, 2018
  
  e51ad99e
- Removed command.py that was not supposed to be there · 0c1575dd
  LANORE Vincent authored Jul 20, 2018
  
  0c1575dd
- Removed hypotheses for this weekend's run · 5aebfca7
  LANORE Vincent authored Jul 20, 2018
  
  5aebfca7
- forgotten script · 73471609
  Carine Rey authored Jul 20, 2018
  
  73471609