Commits · cbd1dfbcbb5d9201ff721f6cbfc97ba7cf61972f · Martin Larralde / LightMotif · GitLab

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Mar 08, 2024
- Streamline use of pipelined functions in `lightmotif-py` · cbd1dfbc
  Martin Larralde authored 1 year ago
  
  cbd1dfbc
- Add simple API to sequence and matrix types internally using a dispatch `Pipeline` · 174a5e0c
  Martin Larralde authored 1 year ago
  
  174a5e0c
- Make `EncodedSequence.stripe` use a `Pipeline` internally · 63d41d1b
  Martin Larralde authored 1 year ago
  
  63d41d1b
- Fix code issues with `cargo clippy` · 411c96d6
  Martin Larralde authored 1 year ago
  
  411c96d6
- Add constructor for Python `ScoringMatrix` class · f7862877
  Martin Larralde authored 1 year ago
  
  f7862877
- Make sure `lightmotif-py` computes the right p-values · 093889bc
  Martin Larralde authored 1 year ago
  
  093889bc
- Clear dual-licensing of the `lightmotif-py` depending on the TFM-PVALUE dependency · ec8d85ea
  Martin Larralde authored 1 year ago
  
  ec8d85ea
- Add support for optional TFMPvalue interface in Python bindings · e85eb753
  Martin Larralde authored 1 year ago
  
  e85eb753
Jan 28, 2024
- Update `cibuildwheel` used in Actions workflows to latest release · 31aab51f
  Martin Larralde authored 1 year ago
  
  31aab51f
Dec 15, 2023
- Implement `FromIterator<A::Symbol>` for `EncodedSequence<A>` · fd2c564a
  Martin Larralde authored 1 year ago
  
  fd2c564a
- Add `Background` constructor computing frequencies from an array of symbol counts · 6e4d37c9
  Martin Larralde authored 1 year ago
  
  6e4d37c9
- Add `Background` constructor counting symbol occurences in a single sequence · 7acbd712
  Martin Larralde authored 1 year ago
  
  7acbd712
- Add `Background` constructor counting symbol occurences in several sequences · 1339bddc
  Martin Larralde authored 1 year ago
  
  1339bddc
- Add trait to count the number of symbol occurences in an arbitrary collection · b5ac2896
  Martin Larralde authored 1 year ago
  
  b5ac2896
- Add methods to compute the entropy and information content of a `CountMatrix` · 0a68afc6
  Martin Larralde authored 1 year ago
  
  0a68afc6
- Add `matrix` accessor to all matrix types in `lightmotif::pwm` · 1249af5f
  Martin Larralde authored 1 year ago
  
  1249af5f
- Fix `PartialEq` for `DenseMatrix` to only compare equality of data · 1e42f62f
  Martin Larralde authored 1 year ago
  
  1e42f62f
Dec 14, 2023
- Fix handling of unknown residues in `permute` impl of `Score` for `Avx2` · 72f19cc7
  Martin Larralde authored 1 year ago
  
  72f19cc7
- Allow indexing a `StripedSequence` to access symbols sequentially · 6b06ad64
  Martin Larralde authored 1 year ago
  
  6b06ad64
Dec 13, 2023
- Bump Python versions in `python.yml` Actions workflow · 828d3adc
  Martin Larralde authored 1 year ago
  
  828d3adc
- Fix description of `lightmotif-io` in `Cargo.toml` [ci skip] · 06359d87
  Martin Larralde authored 1 year ago
  
  06359d87
- Release v0.6.0 · 80ed550b
  Martin Larralde authored 1 year ago
  
  View commits for tag v0.6.0 v0.6.0
  
  80ed550b
- Add a disclaimer that `lightmotif-transfac` is deprecated · b23e324c
  Martin Larralde authored 1 year ago
  
  b23e324c
- Improve documentation of `lightmotif-tfmpvalue` crate · 3033d632
  Martin Larralde authored 1 year ago
  
  3033d632
- Compute optimal matrix column permutations in `TfmPvalue` · e135e36e
  Martin Larralde authored 1 year ago
  
  e135e36e
- Use a fast hashing algorithm for `i64` keys in `lightmotif-tfmpvalue` · 723ed024
  Martin Larralde authored 1 year ago
  
  723ed024
- Invert decay in `lightmotif-tfmpvalue` to reduce rounding errors in granularity · 64b52aa0
  Martin Larralde authored 1 year ago
  
  64b52aa0
- Add `lightmotif-io` crate to the crates published in `rust.yml` Actions workflow · 103f0caf
  Martin Larralde authored 1 year ago
  
  103f0caf
- Fix outdated imports in `lightmotif-io` tests · 0e0ff350
  Martin Larralde authored 1 year ago
  
  0e0ff350
- Add benchmark for the JASPAR 2016 parser of `lightmotif-io` · a60f0fd7
  Martin Larralde authored 1 year ago
  
  a60f0fd7
- Add `README.md` file to `lightmotif-io` · fbb3645a
  Martin Larralde authored 1 year ago
  
  fbb3645a
- Remove code from `lightmotif-transfac` and re-export `lighmotif-io` TRANSFAC module · 63e3d260
  Martin Larralde authored 1 year ago
  
  63e3d260
- Move TRANSFAC parser with other parser in `lightmotif-io` crate · 4e680bb3
  Martin Larralde authored 1 year ago
  
  4e680bb3
Dec 12, 2023
- Make `ScoringMatrix::max_score` and `ScoringMatrix::min_score` ignore `N` column · 3a734572
  Martin Larralde authored 1 year ago
  
  3a734572
- Add parser implementation for JASPAR 2016 count matrices · c19c3686
  Martin Larralde authored 1 year ago
  
  c19c3686
- Add documentation for the UniPROBE record parser · 0d3b7ca0
  Martin Larralde authored 1 year ago
  
  0d3b7ca0
- Add methods to get frequencies from a TRANSFAC `Record` · 993f9ef4
  Martin Larralde authored 1 year ago
  
  993f9ef4
- Make data matrix optional in TRANSFAC `Record` · 03890b44
  Martin Larralde authored 1 year ago
  
  03890b44
- Rewrite TRANSFAC parser to support frequency matrices · b62696c2
  Martin Larralde authored 1 year ago
  
  b62696c2
- Add basic line-based parser for UniPROBE matrices · bb83b10e
  Martin Larralde authored 1 year ago
  
  bb83b10e