TODO.md

TODOs

• Add DreamDIA scoring model
• Generate concensus chrom traces per transition
• Generate an exectuable

In Progress

Future TODOs?

• raw .d data loading using alphatims api
• Add a bruker .d loader using opentims

Completed

• Fix interactivity reseting when certain options are selecting, protein and peptide selection boxes get reset
• Add unit tests
• Small dataset for testing
• Add colors for different peak boundaries
• Implement plotting PyProphet boundaries and scores
• Add grid plot layout if multiple files are loaded
• scale intensities of individual traces for chromatograms
• Add peak picking using pyopenms
• Major refactoring of code base. For main refactoring branch, see patch/masterRefactor
• raw mzML data loading
• DIA-NN results inspection on the raw data
• Make available on PyPi closer to time of publication
• Docker / or just ssh port
• Add gauss smoothing to visualization display. See plotter.py#L169 and plotting_ui.py#L52
• Add public base conformer model - added code, need to upload model