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Multi-omic data integration software tools | Pathway analysis

PheNetic
Web

PheNetic

A user-friendly web server for inferring a sub-network based on probabilistic…

A user-friendly web server for inferring a sub-network based on probabilistic logical querying. PheNetic extracts from an interactome, the sub-network that best explains genes prioritized through a…

JIVE
Desktop

JIVE Joint and Individual Variation Explained

Allows general decomposition of variation for the integrated analysis of…

Allows general decomposition of variation for the integrated analysis of datasets. JIVE decomposes a dataset into a low-rank approximation capturing joint structure between data types, low-rank…

pwOmics
Desktop

pwOmics

A straightforward approach for the integrative analysis of data from different…

A straightforward approach for the integrative analysis of data from different high-throughput technologies based on pathway and interaction models from public databases. pwOmics performs…

NaDH
Dataset

NaDH Nicotiana attenuata Data Hub

Integrates and visualizes genomic, phylogenomic, transcriptomic and metabolomic…

Integrates and visualizes genomic, phylogenomic, transcriptomic and metabolomic data in N. attenuata. NaDH currently hosts collections of predicted protein coding sequences of 11 plant species,…

SAMNetWeb
Web

SAMNetWeb Simultaneous Analysis of Multiple Networks

A web-based tool that enables functional enrichment analysis and visualization…

A web-based tool that enables functional enrichment analysis and visualization of high-throughput datasets. SAMNetWeb can analyse two distinct data types (e.g. mRNA expression and global proteomics)…

Meta-SVM
Desktop

Meta-SVM

Achieves the purpose of meta-analysis as jointly leveraging multiple omics…

Achieves the purpose of meta-analysis as jointly leveraging multiple omics data. Meta-SVM is a meta-analytic support vector machine (SVM) that can accommodate multiple omics data, making it possible…

Plant MetGenMAP
Web

Plant MetGenMAP

Identifies significantly altered biochemical pathways and highly affected…

Identifies significantly altered biochemical pathways and highly affected biological processes. Plant MetGenMAP is an easy-to-use, powerful analysis system that supports many functions of systems…

Mergeomics
Web
Desktop

Mergeomics

A computational pipeline to retrieve biological pathways, gene networks, and…

A computational pipeline to retrieve biological pathways, gene networks, and central regulators critical for disease development. The Mergeomics web server pre-populates a wide range of publically…

BioVLAB-mCpG-SN…
Web

BioVLAB-mCpG-SNP-EXPRESS

Enables to examine the multi-omics integrated analysis and supplies users a way…

Enables to examine the multi-omics integrated analysis and supplies users a way to study their own multi-omics data. It works on the integrated analysis of gene expression, DNA methylation, and…

Lemon-Tree
Desktop

Lemon-Tree

Implements state-of-the-art ensemble methods for module network inference.…

Implements state-of-the-art ensemble methods for module network inference. Lemon-Tree is a “one-stop shop” software suite for module network inference based on previously validated algorithms.…

rMKL-LPP
Desktop

rMKL-LPP Regularized Multiple Kernel Learning Locality Preserving Projections

Allows to integrate different data types. rMKL-LPP is an extension of the…

Allows to integrate different data types. rMKL-LPP is an extension of the multiple kernel learning with dimensional reduction (MKL-DR) method. The Locality Preserving Projections (LPP) allows to…

BCC
Desktop

BCC Bayesian Consensus Clustering

Simultaneously models the dependence and the heterogeneity of various data…

Simultaneously models the dependence and the heterogeneity of various data sources. BCC is a flexible clustering approach that models both an overall clustering and a clustering specific to each data…

SteinerNet
Web

SteinerNet

Provides a convenient tool for using a powerful constrained optimization method…

Provides a convenient tool for using a powerful constrained optimization method to reconstruct signaling and response pathways by integrating multiple ‘omic’ data. SteinerNet seeks a network…

MathIOmica
Desktop

MathIOmica

A Mathematica package written in the Wolfram Language that provides…

A Mathematica package written in the Wolfram Language that provides bioinformatics utilities for analyzing dynamic omics datasets. MathIOmica addresses the necessity to integrate multiple omics…

PSDF
Desktop

PSDF Patient-Specific Data Fusion

Allows to discover prognostic cancer subtypes. PSDF groups patient samples on…

Allows to discover prognostic cancer subtypes. PSDF groups patient samples on the basis of both gene expression and copy number alteration data. It also simultaneously distinguishes, on a…

Omics…
Desktop

Omics Integrator

Detects putative underlying molecular pathways. Omics Integrator allows…

Detects putative underlying molecular pathways. Omics Integrator allows integration of transcriptomic data together with other omic data using interactome data. It permits expression analysis and…

CoxPath
Algorithm

CoxPath

Generates patient-specific predictions for the time to recurrence and survival,…

Generates patient-specific predictions for the time to recurrence and survival, along with outcome risk predictions. CoxPath model is a path following algorithm for the L1-regularized Cox…

sRDA
Desktop

sRDA Sparse Redundancy Analysis

Permits analysis for high dimensional genetic and genomic data. sRDA is an…

Permits analysis for high dimensional genetic and genomic data. sRDA is an algorithm that can identify multiple latent variables associated with the explanatory and response data set, with high…

MARIO
Desktop

MARIO MArkov Random fields to Integrate Omics variables

Classifies genes as differential or not differential based on a generalized…

Classifies genes as differential or not differential based on a generalized correlation measure for multiple sequencing-based genomic variables. MARIO is a hierarchical Bayesian model approach for…

FSMKL
Desktop

FSMKL

A variety of learning strategies to boost prediction performance based on the…

A variety of learning strategies to boost prediction performance based on the use of all available data. We consider data integration via the use of multiple kernel learning supervised learning…

mixOmics
Desktop

mixOmics

An R package dedicated to the exploration and the integration of highly…

An R package dedicated to the exploration and the integration of highly dimensional data sets. A strong focus is given to graphical representation to better understand the relationships between the…

IIS
Web

IIS Integrated Interactome System

An integrative platform with a web-based interface, which integrates four…

An integrative platform with a web-based interface, which integrates four different modules for processing, annotation, analysis and visualization of the interaction profiles of proteins/genes,…

AskOmics
Desktop

AskOmics

Allows researchers to integrate data from tab delimited file into a Resource…

Allows researchers to integrate data from tab delimited file into a Resource Description Framework (RDF) database without knowledge in database management. AskOmics permits users to construct visual…

multiOmicsViz
Desktop

multiOmicsViz

Calculates the spearman correlation between the source omics data and other…

Calculates the spearman correlation between the source omics data and other target omics data. multiOmicsViz identifies the significant correlations and plots the significant correlations on the heat…

bioCancer
Desktop

bioCancer

Allows Cancer Genomics Data analysis and visualization. bioCancer is listening…

Allows Cancer Genomics Data analysis and visualization. bioCancer is listening user setting. Results update immediately when inputs are changed. It focuses on Cancer Genomics data visualisation and…

Grinn
Desktop

Grinn

Contains an internal graph database (Neo4j), and an R package for -omic…

Contains an internal graph database (Neo4j), and an R package for -omic studies. The graph database incorporates data from several databases including KEGG, SMPDB, HMDB, REACTOME, CheBI, UniProt and…

WPBS
Desktop

WPBS Weighted Power Biological Score

Represents a weighted power scoring framework. The WPBS method entails: (1)…

Represents a weighted power scoring framework. The WPBS method entails: (1) extraction of pairwise similarity of yeast Saccharomyces cerevisiae genes, (2) separately rescoring the similarities,…

seqxrefget
Desktop

seqxrefget

Retrieves all cross-referenced data for a sequence entry. seqxrefget is a…

Retrieves all cross-referenced data for a sequence entry. seqxrefget is a command line program from EMBOSS. It is part of the "Data retrieval: Sequence data" command group. A list of…

GeneticInterPre…
Desktop

GeneticInterPred

Predicts synthetic genetic interactions (SGI) by combining functional and…

Predicts synthetic genetic interactions (SGI) by combining functional and topological properties of functional gene network (FGN). GeneticInterPred is a semi-supervised learning (SSL) prediction…

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