Multi-omics data integration
- DLMM: Integrative analysis of DNA copy number and mRNA expression data.
- PECA: Protein expression control analysis for gene expression regulation.
- metaArray: Meta-analysis of microarray data sets.
- PTMscape: an open source tool to predict generic post-translational modifications and map hotspots of modification crosstalk.
- iOmicsPASS: Integrative -omics approach for predictive analysis of cancer subtypes with sub-network signatures.
- 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) .
- MetMatch: Database search engine for untargeted metabolomics (led by Scott Walmsley, U Colorado Denver).
- MetaboDIA: spectral library and data extraction for DIA-MS in metabolomics.
Genome-wide location studies