Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)
COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.
A project for exploring differentially active signaling paths related to proteomics datasets
PHOsphoproteomic dissecTiOn using Networks
Analytical R Tools for Mass Spectrometry
Estimate PTM hotspots in protein sequence alignments
An Ensemble Bioinformatic Platform to Empower Interactive Analysis of Quantitative Phosphoproteomics.
PhosNetVis is a web-based platform for integrated kinase enrichment analyses and interactive 2D/3D network visualizations of phosphoproteomics datasets.
DeepRescore2: deep learning prediction boosts phosphoproteomics-based discoveries through improved phosphopeptide identification
Clusters phosphoproteomics data based on a combination of the sequence information and abundance changes over conditions.
Some phosphoproteomics useful notebooks and sources
PhosphoFind provides functions to identify phosphorylation positions (aminoacid number in proteins) in phosphoproteomics experiments.
Custom analysis of in vitro circadian proteomics and phosphoproteomics using multiple sets of 10plex TMT with two genotypes
It assigns the phosphorylation site in protein
Python pipeline to build empirical kinase networks and identify kinase signalling communities from quantitative phosphoproteomics data.
Phosphorylation landscape on time-resolved SYR1-dependent systemin signaling pathway
R codes for processing MS data
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