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. 

iOmicsPASS+: Integrative analysis of multi-omics data with data-driven network identification. 

PARPROX: Computationally scalable regression modeling with flexible group-wise variable selection

HP-ACCORD: Ultrahigh-dimensional gaussian graphical model estimation

Computational metabolomics and lipidomics

MetaboKIT: comprehensive toolkit for data processing of DDA and DIA mass spectrometry analysis for metabolomics (upgrade of MetaboDIA)

MRMkit: fast and accurate data extraction and normalization for quantitative metabolomics with targeted mass spectrometry

DIMSkit: a new data extraction workflow for direct infusion mass spectrometry




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. 

PRMkit: fast and accurate data extraction and normalization of parallel reaction monitoring (PRM) data

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. 

KSA-2D: 1D and 2D empirical Bayes analysis of differential phosphoproteome analysis

Analysis of interaction proteomics data

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

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

Data visualization

SLIDE: Systems-level Interactive Data Exploration. 

Multi-SLIDE: Visualization of single or multi-omics data with user-driven query

Genomic data analysis

ChIPmeta: Integration of multiple ChIP experiments.

scHMM: Sparsely correlated HMM algorithm for ChIP data analysis. 

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