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wfondrie
Fast and flexible semi-supervised learning for peptide detection in Python
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...
I would like to combine the results of several search engines and perform a re-scoring with mokapot to import the results into the Trans Proteomic Pipeline (TPP). I want to...
This PR fixes the current actions and adds support for dependabot. This also fixes the linting issues in main.
This PR fixes backwards compatibility with 'traditional' pin files (file extension == ".pin", tab delimited, tabs as protein separators, last column == "protein(s)?" caps insensitive). Basically, when detecting that its...
As [discussed here](https://github.com/wfondrie/mokapot/pull/119#discussion_r1646591660), currently when the model is loaded, a StandardScaler is not loaded by newly instantiated. It would be desirable to give the user the flexibility to decide what...
The issue was started by this [discussion](https://github.com/wfondrie/mokapot/pull/119#discussion_r1646580990) regarding MSAID's streaming branch. For streaming several chunk sizes are defined and currently hard-coded. It would be desirable to modify them. Best would...
This issue stems from [this discussion](https://github.com/wfondrie/mokapot/pull/119#discussion_r1646603295). MSAID's streaming branch introduces the OnDiskPSMDataset class which is enables the chunk-wise streaming of a PSMDataset and returns this chunks as LinearPSMDataset. To make...
MSAID's streaming feature introduced a regression so that the suffixes of the psms output files are not `psms.txt` anymore but only `psms`. This is not desirable because it makes it...
This https://github.com/wfondrie/mokapot/pull/119 brings SQLite support for MSAID's internal format. This should live outside of (the core) Mokapot. Options: - move this code to MSAID's repos - move this code to...