Multi-omics data integration

DLMM: Integrative analysis of DNA copy number and mRNA expression data.

PECA: Protein expression control analysis for gene expression regulation.

iOmicsPASS: Integrative -omics approach for predictive analysis of cancer subtypes with sub-network signatures.

GPD (Gene-to-Protein-to-Disease framework): a protein-centric data summary approach for association analysis from whole exome sequencing data

    • GPD GitHub sites

Computational metabolomics

MetaboDIA: spectral library and data extraction for DIA-MS in metabolomics.

MetaboKIT: comprehensive toolkit for mass spectrometry-based metabolomics analysis

    • GITHUB repository

Data visualization

SLIDE: Systems-level Interactive Data Exploration.


Differential expression analysis for proteomics data

EBprot: Statistical analysis of labeling-based proteomics data.

mapDIA: Data processing and statistical analysis of data independent acquisition MS data.

QSPEC/QPROT: Statistical protein differential expression analysis for spectral count data.

Analysis of interaction proteomics data

nestedCluster: Biclustering algorithm for affinity purification – quantitative proteomics data.

SAINT suite: Significance analysis of affinity purification-MS data.

Computational proteomics

LuciPHOr: Probabilistic algorithm to control false localization rates of generic PTM from mass spectrometry-based proteomics data.

MSblender: Integration of database search results in peptide identification (led by TJ Kwon, UNIST, Korea) .

PTMscape: an open source tool to predict generic post-translational modifications and map hotspots of modification crosstalk.

Genome-wide location studies

ChIPmeta: Integration of multiple ChIP experiments.

scHMM: Sparsely correlated HMM algorithm for ChIP data analysis.