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Jhsmit / hdxms-datasets Public

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Update formats#16

Merged

Jhsmit merged 35 commits intomasterJhsmit/hdxms-datasets:masterfrom

update_formatsJhsmit/hdxms-datasets:update_formatsCopy head branch name to clipboard

Dec 17, 2025

Conversation Commits35 (35)Checks Files changed

Merged

Update formats#16
Jhsmit merged 35 commits intomasterfrom
update_formats

Commits

Commits on Dec 9, 2025

add reading hd examiner peptide pool
Jhsmit
committed
prepare for identify by path
Jhsmit
committed

Commits on Dec 10, 2025

add protein filter field
Jhsmit
committed
refactor loader to reader, rework formats
Jhsmit
committed
remove combined schema
Jhsmit
committed

Commits on Dec 11, 2025

fix peptide pool reader and add tests
Jhsmit
committed
add kingfisher HD examiner example file
Jhsmit
committed
refactor peptide pool reader
Jhsmit
committed
refactor: update format handling and improve peptide loading functionality
Jhsmit
committed
example of only reading files
Jhsmit
committed
fix loading datasets example
Jhsmit
committed
add protein field to docs
Jhsmit
committed
add hd examiner peptides files
Jhsmit
committed
cast exposure can also raise ValueError
Jhsmit
committed

Commits on Dec 15, 2025

group by protein and state such that dataframes can be aggregated in batch
Jhsmit
committed
fix hd examiner format identification
Jhsmit
committed
aggregate replicate, cluster and charge count
Jhsmit
committed
add summary function
Jhsmit
committed
add uptake summary table
Jhsmit
committed

Commits on Dec 16, 2025

add load method to formats
Jhsmit
committed
fix format names
Jhsmit
committed
add uptake summary converter
Jhsmit
committed
renew test data with n_charges column
Jhsmit
committed
expand docs on n_charges
Jhsmit
committed
add function to find offset between structure and peptides
Jhsmit
committed
update docstring and allow selecting mutiple columns on join
Jhsmit
committed
make publication title required
Jhsmit
committed
support loading from .zip files
Jhsmit
committed
allow loading form dir also when there is only 1 dataset present
Jhsmit
committed
delete comment
Jhsmit
committed

Commits on Dec 17, 2025

pass exception when format is not a string
Jhsmit
committed
formatting
Jhsmit
committed
remove unused code from zip example
Jhsmit
committed
check for stringIO type, format file
Jhsmit
committed
add loading .zip test
Jhsmit
committed

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