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
MetaboDIA: spectral library and data extraction for DIA-MS in metabolomics.
MetaboKIT: comprehensive toolkit for mass spectrometry-based metabolomics analysis
- GITHUB repository
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.
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.