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9a00504
ignore dev nb
zix-xiao Dec 19, 2024
e3bd45a
update construct_dict to support mzML input
zix-xiao Dec 19, 2024
9b97318
update inference function for data without IMS dimension
zix-xiao Dec 19, 2024
6cd530d
add example
zix-xiao Dec 19, 2024
889d203
Stop tracking ignored files in notebooks folder
zix-xiao Dec 19, 2024
6693f01
stop tracking ignores in exp_configs
zix-xiao Dec 19, 2024
6c44527
move src code to swaps
zix-xiao Jan 22, 2025
ce310f9
add license
zix-xiao Jan 22, 2025
f6f3d81
update project specs
zix-xiao Jan 22, 2025
67a8acb
fix reference rt values, seperate calibrated retention time as _exp a…
zix-xiao Jan 11, 2025
3c7086c
rename linear regression between ref and exp im from "pred_lr" to "al…
zix-xiao Jan 11, 2025
80ed5f6
add config for revision experiments
zix-xiao Jan 21, 2025
6385c9b
add switch case to catch undefind cases
zix-xiao Jan 21, 2025
df73a95
generalize support for not using Decoy
zix-xiao Jan 21, 2025
7c9fcf0
add support for "ref" and "align_lowess"
zix-xiao Jan 21, 2025
61ce822
fix lr alignment of im out of bound error
zix-xiao Jan 21, 2025
8d4198e
fix rt out of bound error
zix-xiao Jan 21, 2025
bd4ec67
add support for ps test set eval without decoy and scoring model
zix-xiao Jan 21, 2025
b56d086
add support for using auto generated ps dir activation result
zix-xiao Jan 21, 2025
59465b4
update intensity by im range
zix-xiao Jan 21, 2025
75689ea
update plotting utils
zix-xiao Jan 21, 2025
a47209b
update options for IM_REF
zix-xiao Jan 21, 2025
a1da0bf
add support for not using decoy
zix-xiao Jan 21, 2025
672b371
skip inference if act_ps already exists
zix-xiao Jan 21, 2025
31b1b07
add experiment for additional experiment for first revision
zix-xiao Jan 21, 2025
23b8097
add experiment for additional experiment for first revision
zix-xiao Jan 21, 2025
7c1f6bc
update env specs
zix-xiao Jan 21, 2025
b57b277
remove early dev without IM support
zix-xiao Jan 22, 2025
37df23c
clean up dependencies management
zix-xiao Jan 22, 2025
5fd5748
add test configs
zix-xiao Jan 22, 2025
2cfc589
update notebook
zix-xiao Jan 22, 2025
f16341c
reorg source code into swaps module
zix-xiao Jan 22, 2025
1dc604d
ignore peak detection config
zix-xiao Jan 22, 2025
cf3707f
update test config
zix-xiao Jan 22, 2025
328c9d3
update project specs
zix-xiao Jan 22, 2025
bd31c34
update readme for the new project setup
zix-xiao Jan 22, 2025
d07c50f
Merge branch 'multi_output_PS_model' into swa_for_xic
zix-xiao Jan 22, 2025
17f4b91
add pyteomics for processing mzml
zix-xiao Jan 22, 2025
bf29d72
update prepare_dict for seperating w/o ims cases
zix-xiao Jan 22, 2025
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12 changes: 3 additions & 9 deletions .gitignore
Original file line number Diff line number Diff line change
@@ -1,21 +1,15 @@
._.DS_Store
.DS_Store
*.pyc
notebooks/models/*
notebooks/wandb/*
notebooks/dev*.ipynb
notebooks/ref*.ipynb
notebooks/exp*.ipynb
notebooks/*.txt
notebooks/*
!notebooks/dev_90_ayla_test.ipynb
wandb/*
.vscode/*
notebooks/my_dir/*
test/test.py
output.png
output.svg.png
array_param/*
notebooks/*.png
archieved/ScanByScan.py
archieved/*
scripts/slurm_job_swaps_gpu.sh
_archieved/*
environment_linux64.yaml
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17,507 changes: 17,507 additions & 0 deletions notebooks/dev_90_ayla_test.ipynb

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