Aggregate into bruker branch #17
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jspaezp
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Jun 4, 2023
* (wip) changed ims collapsing * (wip) changed parameters on IMS collapsing and deisotoping * (wip) fixed bug where empty spectra would crash the program * (wip) further improvememet on timstof data * (wip) changed location for deisotoping * (wip) adding precursor information to the searches * new deisotoping abstractions * initial rt model * (wip,bugfix) changed neighborhood search and fixed splitting of TIMS spectra * (bugfix) fixed bug on deisotoping indexing * (wip) progress todards merge * (wip) ruff compliance * (wip) ruff compliance * (wip) prettyfied deisotoping testing * added ims and rt info to the output file * removed some dead code * Added run-level mokapot and updated rt * better top rank handling * remove search_utils.py * removed legacy make pin function * Add sklearn * Aggregate into bruker branch (#17) * initial rt model * Added run-level mokapot and updated rt * better top rank handling * remove search_utils.py * removed legacy make pin function * Add sklearn --------- Co-authored-by: Carolyn Allen <callen@talus.bio> Co-authored-by: William Fondrie <fondriew@gmail.com> * Updated imputer models and added tests * partial migration to polars and partial implementation of caching * further additions to spectrum caching * Add decoys * (wip,bugfix,feature) initial addition of dvc workflows for benchmarking and logging sinking for mokapot * Drafted global FDR and alignment * Update to work with dataframe inputs as well * (wip) addition of fragment position information * Added base interface * Fixed interface tests * moved test * added correlation filtering, parquet caching and improvement of data pipeline * updated dvc * updated dvc run info * updated dvc run info * minor docsting change * updated run info * updated metrics and fixed mzml * Updated base interface * updated plots and metrics * reverted accidental changes from branch merge and test fixing * (experimental) change in the scoring intensities * added precursor removal and minor change in scoring function * added narrow window dia results * updated dvc run information for orbi data * ruff compliance * updated linting and actions * updated dvc results --------- Co-authored-by: = <=> Co-authored-by: Carolyn Allen <callen@talus.bio> Co-authored-by: William Fondrie <fondriew@gmail.com>
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