Useful data analysis tools

Gene Ontology and/or pathway analyses

DAVID : Pathway and Gene Ontology analyses

Metascape : Gene Ontology and pathway analysis

PANTHER : Gene Ontology analysis

Webgestalt : Gene Set analysis

ARACNe : Reconstruction of cellular networks

WGCNA : Weighted correlation network analysis

KDDN : Knowledge-fused Differential Dependency Network

PathVisio : Biological pathway editor

Cytoscape : Network data integration, analysis and visualization

 

Interactome analyses

STRING : Interactome analysis

XLinkDB : Database and tools to store, visualize and predict protein interaction topologies

XLINKX : Software for protein crosslinking analysis

MeroX : Software for protein crosslinking analysis

Databases

PhosphoSitePlus : PTM database

dbPTM : Integrated resources for protein PTMs

ProteomicsBrowser : Visualization of protein PTM data

Human Proteome Map : Human tissue-dependent protein expression map

Proteomics DB : Human tissue-dependent protein expression map

Human Protein Atlas : Human protein expression map integrating data from multiple sources

CSF Proteome Resource : Database for cerebrospinal fluid proteins

EFLM Biological Variation Database : Database for biological variations

Proteome data analysis

MaxQuant : Software for proteome database search

OpenMS : Software for LC/MS data management and analysis

DIA-NN : A universal automated software suite for DIA proteomics data analysis

DO-MS : Data-driven optimization of mass spectrometry methods

DART-ID : A computational tool that leverages reproducible retention time to increase confident peptide ID

RawBeans : DDA data quality control tool

MSFragger : Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

IceR : Quantitative label-free proteomics workflow

ChemCalc : A web-based App for polymer mass spectrometry data interpretation

ProMetIS : Integrative analysis of proteome and metabolome data

pGlyco3 : Glycoproteome analysis software

StrucGP : De novo structural sequencing of site-specific N-glycan on glycoproteins

LFQ-Analyst : Interactive web-platform to analyze and visualize proteomics data processed with MaxQuant

Amica : Interactive web-based platform that accepts proteomic input files

MhcVizPiep : QC software for immunopeptidome

EggNOC-mapper : Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale

PRM-LIVE : Real time RT alignment for PRM. Link to the paper

MS_Piano : Fast and reliable annotation of CID spectra from N-glycopeptides

RWHN_Phosphoproteomics : Inference of the function of individual phosphorylation sites using random walks on heterogenous networks (RWHN)

ProteoSushi : To biologically annotate and quantify multiple PTMs on proteins

OptiMissP : To evaluate missingness in DIA data

Targeted proteome analysis

PeptideAtlas : Compendium of peptides identified in a large set of mass spectrometry data

Picky : PRM and SRM designer tool

Skyline : Software for targeted peptide analysis

Statistical analysis

Perseus : Software for data analysis

SIMCA : Software for multivariate analysis

Anaconda : Data science tool kit

MetaboAnalyst : Statistical analysis and metabolomic data analysis

StatPro : Statistical data analysis including P values, FDR, Cohen's d, fold change, correlation and AUC

Randomizer : Randomization of sample order

Block randomization : Randomization of sample order with multiple blocks

BlackSheep : R package for differential extreme value analysis (outlier analysis)

 

Genome data analysis analysis

Genome Browser : Interactive visualization of genomic data

DNA sequence analysis software : DNA sequence analysis software from Johns Hopkins Center for Computational Biology

Broad Institute software : Data, software and tools from Broad Institute

Expasy : Swiss bioinformatics resource portal

EMBL tools : Molecular data resources maintained by the European Bioinformatics Institute

 

Miscellaneous

AMP-PD : The Accelerating Medicine Partnership in Parkinson’s Disease

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