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
MetaNetwork : A GUI version of WGCNA
KDDN : Knowledge-fused Differential Dependency Network
PathVisio : Biological pathway editor
Cytoscape : Network data integration, analysis and visualization
Enrichr : Analyses for Pathways, Ontologies, Diseases, Cell types
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
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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
BRAINcode Project : Database for the human neuronal genome and transcriptome
OpenProt : Protein databases created by a comprehensive annotation of predicted coding sequences on all transcripts
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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
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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
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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)
ClinCalc : Sample size calculator
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Transcriptome analysis
VoxHunt : Systematic comparison of single-cell transcriptome data to the Allen Brain Atlas data
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Genome data 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
