phosphoproteomics

saezlab/cosmosR

COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.

PathwayAndDataAnalysis/causalpath

A project for exploring differentially active signaling paths related to proteomics datasets

jdrudolph/photon

PHOsphoproteomic dissecTiOn using Networks

biodavidjm/artMS

Analytical R Tools for Mass Spectrometry

evocellnet/ptm_hotspots

Estimate PTM hotspots in protein sequence alignments

liuzan-info/PhosMap

An Ensemble Bioinformatic Platform to Empower Interactive Analysis of Quantitative Phosphoproteomics.

GumusLab/PhosNetVis

PhosNetVis is a web-based platform for integrated kinase enrichment analyses and interactive 2D/3D network visualizations of phosphoproteomics datasets.

bzhanglab/DeepRescore2

DeepRescore2: deep learning prediction boosts phosphoproteomics-based discoveries through improved phosphopeptide identification

fpozoc/phosphoproteomics

Some phosphoproteomics useful notebooks and sources

meyer-lab/DDMC

Clusters phosphoproteomics data based on a combination of the sequence information and abundance changes over conditions.

celiaccb/KinasesCommunityDetection

Python pipeline to build empirical kinase networks and identify kinase signalling communities from quantitative phosphoproteomics data.

davwong47/Circadian-proteomics

Custom analysis of in vitro circadian proteomics and phosphoproteomics using multiple sets of 10plex TMT with two genotypes

lucasragr/Phosphosite_localization

It assigns the phosphorylation site in protein

icervenka/phosphopep

RafRomB/PhosphoFind

PhosphoFind provides functions to identify phosphorylation positions (aminoacid number in proteins) in phosphoproteomics experiments.

ryuhjinahn/Protocols_process_MS_data

R codes for processing MS data

shibalili/systemin-project

Phosphorylation landscape on time-resolved SYR1-dependent systemin signaling pathway