Commits · ddcc808f49d173fc955cb50778b90be31919be43 · Lannoy, Carlos de / baseLess · GitLab

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Nov 14, 2022
- Added analysis for guppy accuracy over time · ddcc808f
  Noordijk, Ben authored 2 years ago
  
  ddcc808f
- Small implementation changes. · f86c2cf2
  Noordijk, Ben authored 2 years ago
  f86c2cf2
May 04, 2022
- Balanced dataset for all species is now used to calculate performance. Also... · 2d27b6f3
  Noordijk, Ben authored 3 years ago
  2d27b6f3
Apr 26, 2022
- Baseless cutoff at 55% of kmers and some minor refactoring · d6ed77cb
  Noordijk, Ben authored 3 years ago
  
  d6ed77cb
Apr 15, 2022
- Calculate accuracies for all folds · bfff3222
  Noordijk, Ben authored 3 years ago
  
  bfff3222
Apr 14, 2022
- Bugfixed inference · c023f2ba
  Noordijk, Ben authored 3 years ago
  
  c023f2ba
- Model now outputs fraction of found kmers · 868f457e
  Noordijk, Ben authored 3 years ago
  
  868f457e
- Changed default kmer cutoff · 591b114f
  Noordijk, Ben authored 3 years ago
  
  591b114f
- Updated help message of --parameter-file · 6cb2159e
  Noordijk, Ben authored 3 years ago
  
  6cb2159e
Apr 12, 2022
- Made ugly way to only look at balanced datasets · 87ac782b
  Noordijk, Ben authored 3 years ago
  
  87ac782b
- Fixed memory issue in run_inference_naive.py · cbd5374f
  Noordijk, Ben authored 3 years ago
  
  cbd5374f
Apr 08, 2022
- Implemented functional API for compile_model.py · abd13467
  Noordijk, Ben authored 3 years ago
  
  abd13467
- Bugfix and modified implementation · 5ef8a1c6
  Noordijk, Ben authored 3 years ago
  
  5ef8a1c6
- Find optimal cutoff and print PR curves for baseless inference on sample · 950c8699
  Noordijk, Ben authored 3 years ago
  
  950c8699
Apr 07, 2022
- Changed signature of scan_one_file · 01251377
  Noordijk, Ben authored 3 years ago
  
  01251377
- Refactoring for import statement · 50b71472
  Noordijk, Ben authored 3 years ago
  
  50b71472
Apr 05, 2022
- Code to determine optimal cutoff based on k-fold · 0a66b1bc
  Noordijk, Ben authored 3 years ago
  
  0a66b1bc
Apr 04, 2022
- Added implementation to create in silico samples of reads · bddcb6a0
  Noordijk, Ben authored 3 years ago
  
  bddcb6a0
- Renamed compare_accuracy.py to compare_accuracy_per_read.py · 6b430cbc
  Noordijk, Ben authored 3 years ago
  
  6b430cbc
Apr 01, 2022
- Changed order of tools in bar chart · 2a857b1c
  Noordijk, Ben authored 3 years ago
  
  2a857b1c
- Updated inference procedure of deepnano and guppy to increase their performance · 3f2a6183
  Noordijk, Ben authored 3 years ago
  
  3f2a6183
- Changed some parameters · e541895b
  Noordijk, Ben authored 3 years ago
  
  e541895b
- Now handles missing neural networks correctly · 14d39945
  Noordijk, Ben authored 3 years ago
  
  14d39945
- Changed baseless_output to other directory · 08e3a1ff
  Noordijk, Ben authored 3 years ago
  
  08e3a1ff
- 8+9-mer models now implemented · e1c52b9f
  Noordijk, Ben authored 3 years ago
  
  e1c52b9f
Mar 30, 2022
- Started 8+9-mer implementation · 9c9f3adc
  Noordijk, Ben authored 3 years ago
  
  9c9f3adc
- Now use 95% alignment cutoff for guppy · 2c931ac3
  Noordijk, Ben authored 3 years ago
  
  2c931ac3
Mar 14, 2022
- Updated accuracy comparison to look at 9mer output · 8d3ae11c
  Noordijk, Ben authored 3 years ago
  
  8d3ae11c
- Reverted threshold to 6.21 · ad90943f
  Noordijk, Ben authored 3 years ago
  
  ad90943f
Mar 04, 2022
- compile_model.py now works for 9mers in target · 78f7a1ed
  Noordijk, Ben authored 3 years ago
  
  78f7a1ed
Mar 02, 2022
- Added bugfix for out of memory errors · b8906533
  Noordijk, Ben authored 3 years ago
  
  b8906533
Feb 25, 2022
- Changed default max number of positive examples and hardcoded paths to some objects · d4d0cc70
  Noordijk, Ben authored 3 years ago
  
  d4d0cc70
Feb 15, 2022
- Bugfixes for writing to file · d49f063f
  Noordijk, Ben authored 3 years ago
  
  d49f063f
Feb 14, 2022
- K-mer counting now works for any size of k · 108f5983
  Noordijk, Ben authored 3 years ago
  
  108f5983
Jan 28, 2022
- Docstring and formatting changes · 71765e40
  Noordijk, Ben authored 3 years ago
  
  71765e40
- Added parallelization · 968e70b9
  Noordijk, Ben authored 3 years ago
  
  968e70b9
Jan 26, 2022
- Lowered max_tries to 25 per k-mer · 3fde8aad
  Noordijk, Ben authored 3 years ago
  
  3fde8aad
- Added confirmation message after loading initial kmers · a4a29762
  Noordijk, Ben authored 3 years ago
  
  a4a29762
- Now change all kmers for 10 rounds, max sw sim 7 · 4d9c23ac
  Noordijk, Ben authored 3 years ago
  
  4d9c23ac
- Can now provide list of sequences to initiate from · a7dcaffe
  Noordijk, Ben authored 3 years ago
  
  a7dcaffe