Candycrunch

Change Log
general
- updated package to the current `glycowork` version (~=1.20)

analysis
- Generalised monosaccharide mass retrieval
- Added '02X', '02A' dHex cross ring fragments
- Added phosphorylated fragments
- Added '02A', '24X' HexNAc cross ring fragments
- Added '15X', '24X', '25X', '02A', '04A', '14A', '15A', '24A' sialic acid cross ring fragments
- Added '04X', '24X', '35X', '15A', '03A' Hex cross ring fragments

Change Log

general

- updated package to the current `glycowork` version (~=1.1.0)

analysis

- Added '03X', '15X', and '24X' cross ring fragments

cli

- Added `candycrunch_predict` and command line functionality

prediction

- Added `glytoucan_map` to harmonize predicted glycans and display GlyTouCan IDs in outputs
- Added to generation of possible structures by generalising Neu5Ac/Neu5Gc sequence substitutions
- Added to generation of possible structures by generalising GlcNAc/GlcNAc6S sequence substitutions
- Added Neu5Ac isomer deduplication based on Neu5Gc isomers
- Added user defined RT cutoffs `rt_min, rt_max, rt_diff` to narrow downs spectra of interest
- Added functionality to filter out duplicates based on RT
- Added `plot_glycans_excel` support for output excel spreadsheets
- Added `wrap_inference_batch` to run inference on multiple inputs at once and group structures across files

model

- Updated model checkpoint

- updated package to the current `glycowork` version (1.0.1)
- added required dependencies

- fixed indentation in process_mzML_stack

- refactored spectral grouping and averaging
- general code refactoring for readability and efficiency
- filter out very low and very high RT spectra if possible
- added some ancillary functionality, such as combining relative abundances across multiple charge states
- some preparations for eventually accepting glycowork v0.9, including supporting more adducts etc.

- updated model weights (better performance)
- agglomerative clustering for RT grouping
- generalized handling of tag masses in wrap_inference
- calculate ppm error