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Vitek-Lab / MSstatsBioNet Public

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Feature ptm analysis#56

Merged

tonywu1999 merged 23 commits intodevelVitek-Lab/MSstatsBioNet:develfrom

feature-ptm-analysisVitek-Lab/MSstatsBioNet:feature-ptm-analysisCopy head branch name to clipboard

Sep 11, 2025

Conversation Commits23 (23)Checks Files changed

Merged

Feature ptm analysis#56
tonywu1999 merged 23 commits intodevelfrom
feature-ptm-analysis

Commits

Commits on Sep 11, 2025

preliminary setup for ptm analysis
tonywu1999
committed
Add preliminary PTM data and vignette to PTM feature branch
tonywu1999
committed
Code is working with PTM analysis, but analysis is protein specific
tonywu1999
committed
take the max logFC for ranking
tonywu1999
committed
Add ability to filter by phosphorylation interaction and include site info in subnetwork function
tonywu1999
committed
Update vignette to include statement types
tonywu1999
committed
Switch if-else statement for modifications vs other stmt types
tonywu1999
committed
add site information to the edges table for getSubnetworkFromIndra
tonywu1999
committed
add site information in the nodes table
tonywu1999
committed
add hover tooltip first attempt
tonywu1999
committed
hover tool tip fully working now with site info
tonywu1999
committed
finalize ptm overlap hover functionality
tonywu1999
committed
consider scenario where global protein column does not exist
tonywu1999
committed
remove getpathwaysfromindra
tonywu1999
committed
modify PTM vignette
tonywu1999
committed
remove commented code
tonywu1999
committed
tidy up comments
tonywu1999
committed
add visualization in vignette
tonywu1999
committed
ensure protein column is a character and not a factor
tonywu1999
committed
reorder when protein is turned into a character
tonywu1999
committed
remove changed comments
tonywu1999
committed
add multiple PTM sites to site column
tonywu1999
committed
make multiple PTMs compatible in hover tooltip
tonywu1999
committed

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