Add a new Knowledge-Based Analysis tab#2
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MA-Tianrui wants to merge 21 commits intoNesvilab:mainfrom
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…er DE analysis with volcano, ORA, GSVA, and network panels
Perform PTM-SEA with package fast.ssgsea PTM-SEA available for phosphorylation, acetylation, ubiquitnation
make the legend of network figure add color gradient to protein fold change, interaction score enable the highlight of nodes or edges
Add kinase-substrate network tab using PTM-SEA results Replace visNetwork highlightNearest with custom JS for precise node/edge selection Add bait-connected-only filter, dynamic STRING score/FC scales ORA built-in databases now return all contrasts in one run Move minor network params into collapsible advanced settings Remove KEGG Pathway Network tab
UI improvement, including table filters ORA gene set selection: Limited to 2 sets max, specify the overlapping genes Enable ORA set labelling in volcano plot for site-level data
Fix flanking sequence matching bug in KS network Deduplicate PSP vs iKiP kinase sets in KS network
Add a new tab "Kinase activity" under gene set explorer panel, running Z-score kinase activity inference Add a new kinase-substrate database in data folder: curated_library from benchmarKIN, used for performing Z-score
Add a source option for kinase-substrate network to use results from PTM-SEA or z-score interference Implement the volcano plot labeling for z-score result table
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Add a Knowledge-Based Analysis tab for downstream analysis after DE, including: