Multi-omics data integration

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

• • http://sourceforge.net/projects/dlmm/

PECA: Protein expression control analysis for gene expression regulation. 

• • Latest development at https://github.com/PECAplus 

  • Old version of PECA at http://sourceforge.net/projects/pecanalysis/

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

• • https://github.com/cssblab/iOmicsPASS 

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

• • https://github.com/cssblab/iOmicsPASSplus

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

• https://github.com/kose-y/ParProx.jl

Computational metabolomics and lipidomics

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

• • https://github.com/MetaboKit/MetaboKit

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

• • https://github.com/mrmkit/mrmkit

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

• • GitHub page: 

Metaboscan: 

• • GitHub page: 

LipidEF: 

• • GitHub page: 

midar:  

• • GitHub page: 

Computational proteomics

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

• • http://luciphor.sourceforge.net/ 

  • http://luciphor2.sourceforge.net/

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

• • http://sourceforge.net/projects/msblender/

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

• • https://github.com/cssblab/PTMscape/

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

• • GitHub page: to be released

Differential expression analysis for proteomics data

EBprot: Statistical analysis of labeling-based proteomics data.

• • http://sourceforge.net/projects/ebprot/ 

  • http://github.com/cssblab/EBprot

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

• • https://github.com/mapDIA/mapDIA

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

• • http://sourceforge.net/projects/qprot/

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

• • https://github.com/ginnyintifa/KSA2D 

Analysis of interaction proteomics data

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

• • http://sourceforge.net/projects/nestedcluster/

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

• • http://sourceforge.net/projects/saint-apms/

Data visualization

SLIDE: Systems-level Interactive Data Exploration. 

• • Click here for the web version of SLIDE

  • GitHub page: https://github.com/cssblab/SLIDE

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

• • GitHub page: https://github.com/soumitag/multiSLIDE

Genomic data analysis

ChIPmeta: Integration of multiple ChIP experiments.

• • http://sourceforge.net/projects/chipmeta

scHMM: Sparsely correlated HMM algorithm for ChIP data analysis. 

• • http://sourceforge.net/projects/schmm/

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

• • https://github.com/ginnyintifa/GPD