Will Fondrie
Will Fondrie
I noticed that there was no implementation for a `decision_function()` method when using the `Incremental` wrapper. This PR adds a `decision_function()` to the `ParallelPostFit` class and updates an existing test...
Currently mokapot uses the old `numpy.random` functions to control random number generation. We should upgrade to using the new `numpy.random.Generator` interface. Alongside this change, we should add a `random_state` or...
To have truly valid precursor- and peptide-level FDR estimates for data independent acquisition (DIA) results, we need to add support for the peptide competition step described in section 2.4 of...
@jspaezp suggested switching over to [pytest-datadir](https://github.com/gabrielcnr/pytest-datadir) for managing our test data. This would have the benefit of simplifying our test fixtures, making it easier for folks to contribute. The user...
In crosslinking mass spectrometry experiments, we try to detect two peptides that are covalently linked from a single MS2 spectrum. Because the pairs can take various forms (target-target, target-decoy, decoy-decoy),...
It seems as if it should be fairly straightforward to add support for getting metabolomics data through [MetabolomeXchange](http://www.metabolomexchange.org/site/) using their documented [API](http://api.metabolomexchange.org/). I need to do more research to learn...
Polars seems like a promising replacement for Pandas in mokapot that should make things run even faster. https://www.pola.rs/
This is a huge, in-progress PR swapping out the Pandas backend for Polars. The goal is to improve the speed and scalability of mokapot. In addition to this huge change,...
One hindrance to large-scale analyses across many runs is that PSMs from all of the runs must be concatenated and read into memory at the same time. This creates a...
This pull request adds a module for parsing the ELIB and DLIB spectral libraries, `src/ann_solo/sqlite_parsers.py`. These are SQLite3 formats from EncyclopeDIA and are defined [here](https://bitbucket.org/searleb/encyclopedia/wiki/EncyclopeDIA%20File%20Formats). The PR also changes the...