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wilhelm-lab / SWAPS Public

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Swa for xic#2

Draft

zix-xiao wants to merge 39 commits intomulti_output_PS_modelwilhelm-lab/SWAPS:multi_output_PS_modelfrom

swa_for_xicwilhelm-lab/SWAPS:swa_for_xicCopy head branch name to clipboard

Conversation Commits39 (39)Checks Files changed

Draft

Swa for xic#2
zix-xiao wants to merge 39 commits intomulti_output_PS_modelfrom
swa_for_xic

Commits

Commits on Dec 19, 2024

ignore dev nb
zix-xiao
committed
update construct_dict to support mzML input
zix-xiao
committed
update inference function for data without IMS dimension
zix-xiao
committed
add example
zix-xiao
committed
Stop tracking ignored files in notebooks folder
zix-xiao
committed
stop tracking ignores in exp_configs
zix-xiao
committed

Commits on Jan 22, 2025

move src code to swaps
zix-xiao
committed
add license
zix-xiao
committed
update project specs
zix-xiao
committed
fix reference rt values, seperate calibrated retention time as _exp and _ref
zix-xiao
committed
rename linear regression between ref and exp im from "pred_lr" to "align_lr"
zix-xiao
committed
add config for revision experiments
zix-xiao
committed
add switch case to catch undefind cases
zix-xiao
committed
generalize support for not using Decoy
zix-xiao
committed
add support for "ref" and "align_lowess"
zix-xiao
committed
fix lr alignment of im out of bound error
zix-xiao
committed
fix rt out of bound error
zix-xiao
committed
add support for ps test set eval without decoy and scoring model
zix-xiao
committed
add support for using auto generated ps dir activation result
zix-xiao
committed
update intensity by im range
zix-xiao
committed
update plotting utils
zix-xiao
committed
update options for IM_REF
zix-xiao
committed
add support for not using decoy
zix-xiao
committed
skip inference if act_ps already exists
zix-xiao
committed
add experiment for additional experiment for first revision
zix-xiao
committed
add experiment for additional experiment for first revision
zix-xiao
committed
update env specs
zix-xiao
committed
remove early dev without IM support
zix-xiao
committed
clean up dependencies management
zix-xiao
committed
add test configs
zix-xiao
committed
update notebook
zix-xiao
committed
reorg source code into swaps module
zix-xiao
committed
ignore peak detection config
zix-xiao
committed
update test config
zix-xiao
committed
update project specs
zix-xiao
committed
update readme for the new project setup
zix-xiao
committed
Merge branch 'multi_output_PS_model' into swa_for_xic
zix-xiao
committed
add pyteomics for processing mzml
zix-xiao
committed
update prepare_dict for seperating w/o ims cases
zix-xiao
committed

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