Commits · 39b2a868f5a5b1f98459ba440cbfabda3e7cefc6 · Lannoy, Carlos de / baseLess · GitLab

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Jan 21, 2022
- Merge remote-tracking branch 'origin/coa_analysis' into coa_analysis · 39b2a868
  Carlos de Lannoy authored 3 years ago
  
  39b2a868
- coa training works · bf13b447
  Carlos de Lannoy authored 3 years ago
  
  bf13b447
- Merge remote-tracking branch 'origin/coa_analysis' into coa_analysis · 9eda77b2
  Noordijk, Ben authored 3 years ago
  
  # Conflicts: # coa_detection/AbfData.py
  9eda77b2
- Started script to make in silico mixtures · b33e799f
  Noordijk, Ben authored 3 years ago
  
  b33e799f
- Added support for unfiltered examples · 259a7cc8
  Noordijk, Ben authored 3 years ago
  
  259a7cc8
- allow randomly drawing 1 example · 214a9635
  Carlos de Lannoy authored 3 years ago
  
  214a9635
- Merge branch 'coa_analysis' of git.wur.nl:lanno001/baseless into coa_analysis · f8bb3c9e
  Carlos de Lannoy authored 3 years ago
  
  Conflicts: coa_detection/AbfData.py
  f8bb3c9e
- db building works · b29decf4
  Carlos de Lannoy authored 3 years ago
  
  b29decf4
- Added ability to extract unfiltered data · 2bf73b7d
  Noordijk, Ben authored 3 years ago
  
  2bf73b7d
- Test test · 21539ecb
  Noordijk, Ben authored 3 years ago
  
  21539ecb
- Merge remote-tracking branch 'origin/coa_analysis' into coa_analysis · b032b870
  Noordijk, Ben authored 3 years ago
  
  # Conflicts: # coa_detection/AbfData.py
  b032b870
- Added get_pos and get_neg methods · 77b82102
  Noordijk, Ben authored 3 years ago
  
  77b82102
- ABF parsing, plotting, and filtering · b9d3f152
  Noordijk, Ben authored 3 years ago
  
  b9d3f152
- cOA detection general code structure · aa447c3e
  Carlos de Lannoy authored 3 years ago
  
  aa447c3e
Jan 20, 2022
- start abf reading functionality · 201ec87f
  Lannoy, Carlos de authored 3 years ago
  
  201ec87f
Jan 18, 2022
- update abundance estimation benchmark · b2ff940a
  Carlos de Lannoy authored 3 years ago
  
  b2ff940a
Jan 16, 2022
- abundance result analysis · c358f375
  Lannoy, Carlos de authored 3 years ago
  
  c358f375
Jan 12, 2022
- multiple samping abundance estimation benchmark · 81a92966
  Carlos de Lannoy authored 3 years ago
  
  81a92966
- multiple samping abundance estimation benchmark · fd6276e3
  Carlos de Lannoy authored 3 years ago
  
  fd6276e3
Jan 07, 2022
- model accuracy filtering · 36125033
  Lannoy, Carlos de authored 3 years ago
  
  36125033
Dec 28, 2021
- small fixes abundance estimation · 22b33bab
  Lannoy, Carlos de authored 3 years ago
  
  22b33bab
Dec 27, 2021
- add abundance estimation mode · 3f6cd45b
  Lannoy, Carlos de authored 3 years ago
  
  3f6cd45b
Dec 21, 2021
- batch processing · a1aa952f
  Lannoy, Carlos de authored 3 years ago
  
  a1aa952f
Dec 17, 2021
- in 16s validation make training on the fly optional · 6482b41b
  Carlos de Lannoy authored 3 years ago
  
  6482b41b
- ReadTable with queues instead of sqlite · d464a531
  Carlos de Lannoy authored 3 years ago
  
  d464a531
- bug fixes compile_model · 3dc43ac8
  Carlos de Lannoy authored 3 years ago
  
  3dc43ac8
Dec 14, 2021
- fix bug in 16S validtion w premade indices · fb465d95
  Carlos de Lannoy authored 3 years ago
  
  fb465d95
Dec 11, 2021
- allow using pre-made index files in validate_16S · e49000d7
  Lannoy, Carlos de authored 3 years ago
  
  e49000d7
Dec 10, 2021
- update validation routine · d92b49d1
  Carlos de Lannoy authored 3 years ago
  
  d92b49d1
Dec 09, 2021
- switch off complicated k-mer selection process for 16S k-mers · 383bdcc0
  Lannoy, Carlos de authored 3 years ago
  
  383bdcc0
- compile all elements of overarching model in single graph · 0faeea48
  Lannoy, Carlos de authored 3 years ago
  
  0faeea48
Dec 07, 2021
- express k-mer threshold as fraction of total rather than absolute int · 7b649606
  Carlos de Lannoy authored 3 years ago
  
  7b649606
- reduce number of simultaneously running compile_model to avoid mem issues · 13473cca
  Carlos de Lannoy authored 3 years ago
  
  13473cca
Dec 05, 2021
- properly add min-nb-models to compile_model parser · 0e9b2cc7
  Carlos de Lannoy authored 3 years ago
  
  0e9b2cc7
Dec 03, 2021
- Merge branch 'master' of git.wur.nl:lanno001/baseless · 71e55f92
  Carlos de Lannoy authored 3 years ago
  
  71e55f92
Dec 02, 2021
- make min nb models arg, small fixes · dec89520
  Lannoy, Carlos de authored 3 years ago
  
  dec89520
Nov 30, 2021
- overhaul threshold analysis, add precision recall plot · 83e37100
  Lannoy, Carlos de authored 3 years ago
  
  83e37100
- add f1 to summary table · fcdb00a7
  Lannoy, Carlos de authored 3 years ago
  
  fcdb00a7
Nov 29, 2021
- fixes for benchmarking and thresholding · 66da9665
  Lannoy, Carlos de authored 3 years ago
  
  66da9665
Nov 26, 2021
- on the fly training should only pick k-mers from discernible k-mer list · 7cc65f8a
  Lannoy, Carlos de authored 3 years ago
  
  7cc65f8a