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Copy number and gene expression data integration software tools | Genomic array data analysis

Over the last decade, multiple functional genomic datasets studying chromosomal aberrations and their downstream effects on gene expression have accumulated for several cancer types. A vast majority of them are in the form of paired gene expression…
CONEXIC
Desktop

CONEXIC COpy Number and EXpression In Cancer

Integrates matched copy number (amplifications and deletions) and gene…

Integrates matched copy number (amplifications and deletions) and gene expression data from tumor samples to identify driving mutations and the processes they influence. CONEXIC is inspired by Module…

SNF
Desktop

SNF Similarity Network Fusion

A computational method for data integration. Briefly, SNF combines many…

A computational method for data integration. Briefly, SNF combines many different types of measurements (such as mRNA expression data, DNA methylation, miRNA expression and more - clinical data,…

G T A T C G C T A
iGC
Desktop

iGC

Identifies differentially expressed genes driven by Copy Number Alterations…

Identifies differentially expressed genes driven by Copy Number Alterations (CNA) from samples with both gene expression and CNA data. iGC supports multiple input formats and users can define their…

RGCCA
Desktop

RGCCA Regularized and Sparse Generalized Canonical Correlation Analysis

Permits the analysis of several sets of variables (blocks) observed on the same…

Permits the analysis of several sets of variables (blocks) observed on the same group of individuals. RGCCA is a multiblock data analysis that extracts the information which is shared by the J-blocks…

Clusternomics
Desktop

Clusternomics

Identifies groups of samples across heterogeneous datasets. The Clusternomics…

Identifies groups of samples across heterogeneous datasets. The Clusternomics algorithm uses probabilistic modelling to identify the groups and share information across the local and global levels.…

tmle.npvi
Desktop

tmle.npvi

Considering associations between DNA copy numbers and expression levels in…

Considering associations between DNA copy numbers and expression levels in genes is not new. In contrast to these earlier contributions, tmle.npvi does explicitly exploit that DNA copy number…

PREDA
Desktop

PREDA Position RElated Data Analysis

Detects regional variations in genomics data. PREDA implements a procedure to…

Detects regional variations in genomics data. PREDA implements a procedure to analyze the relationships between data and physical genomic coordinates along chromosomes with the final aim of…

SplitThreader
Web
Desktop

SplitThreader

Allows to analyse and visualize genomic rearrangements and copy number…

Allows to analyse and visualize genomic rearrangements and copy number variation (CNV) in cancer genomes. SplitThreader constructs a sequence graph of genomic rearrangements in the sample and uses a…

iCluster
Desktop

iCluster

Provides an integrative clustering method for multi-type genomic data analysis.…

Provides an integrative clustering method for multi-type genomic data analysis. iCluster is a R package that offers an approach based on a joint latent variable model and uses a lasso regression to…

SIGMA2
Desktop

SIGMA2

A system for the integrative genomic multi-dimensional analysis of cancer…

A system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes. Multi-dimensional datasets can be simultaneously visualized and analyzed with…

PINS
Algorithm

PINS Perturbation clustering for data INtegration and disease Subtyping

Provides an alternative to Consensus Clustering, a technique in machine…

Provides an alternative to Consensus Clustering, a technique in machine learning, with the additional ability to integrate multiple types of data. PINS can be used to integrate many other…

RSNF
Desktop

RSNF Robust Similarity Network Fusion

Improves the clustering performance significantly. RSNF is a multi-view…

Improves the clustering performance significantly. RSNF is a multi-view clustering algorithm based on Similarity Network Fusion (SNF) and using robust affine graph construction. This method may be a…

PLRS
Desktop

PLRS Piecewise Linear Regression Splines

Provides flexible modelling of the association between DNA copy number and mRNA…

Provides flexible modelling of the association between DNA copy number and mRNA expression. PLRS is particularly useful for (i) a detailed understanding of the relationship between DNA copy number…

SODEGIR
Desktop
joint_genomics
Desktop

joint_genomics

A non-parametric Bayesian factor model is proposed for joint analysis of…

A non-parametric Bayesian factor model is proposed for joint analysis of multi-platform genomics data. joint_genomics is based on factorizing the latent space (feature space) into a shared component…

remMap
Desktop

remMap REgularized Multivariate regression for identifying MAster Predictors

A method for fitting multivariate response regression models under the…

A method for fitting multivariate response regression models under the high-dimension-low-sample-size setting. remMap is motivated by investigating the regulatory relationships among different…

WebaCGH
Web

WebaCGH Web Array Comparative Genomic Hybridisation

Allows detection of chromosomal gains and losses in a high-resolution format.…

Allows detection of chromosomal gains and losses in a high-resolution format. WebaCGH performs about oligonucleotide microarrays and cDNA. This tool has three different functions: (1) detect…

edira
Desktop

edira

A procedure for an integrated analysis of two different data types that…

A procedure for an integrated analysis of two different data types that searches for genes and genetic regions which for both inputs display strong equally directed deviations from the reference…

DR-Integrator
Desktop

DR-Integrator DNA/RNA-Integrator

A freely-available statistical software tool to perform integrative analyses on…

A freely-available statistical software tool to perform integrative analyses on paired DNA copy number and gene expression data. DR-Integrator identifies genes with significant correlations between…

iBAG
Desktop

iBAG

An integrative Bayesian analysis of genomics data framework for identifying…

An integrative Bayesian analysis of genomics data framework for identifying important genes/biomarkers that are associated with clinical outcome. iBAG uses hierarchical modeling to combine the data…

CNAmet
Desktop

CNAmet

Prioritizes putative cancer driver genes by integrating copy number, DNA…

Prioritizes putative cancer driver genes by integrating copy number, DNA methylation and expression data. Outputs of CNAmet include scores for methylation alteration induced expression, copy number…

DANCE
Desktop

DANCE Deregulation Analysis in Networks of Copy-number-driven Expression

A statistical deregulation model that integrates copy number and expression…

A statistical deregulation model that integrates copy number and expression data of different disease subtypes to jointly model common and differential regulatory relationships. DANCE not only…

integIRTy
Desktop

integIRTy integration using Item Response Theory

Identifies altered genes by using item response theory that allows integrated…

Identifies altered genes by using item response theory that allows integrated analysis of multiple high-throughput assays. When applied to a single assay, integIRTy is more robust and reliable than…

integrOmics
Desktop

integrOmics

Performs integrative analyses of two types of 'omics' variables that…

Performs integrative analyses of two types of 'omics' variables that are measured on the same samples. integrOmics includes a regularized version of canonical correlation analysis to…

Consensus…
Desktop

Consensus Clustering

Provides a method to represent the consensus across multiple runs of a…

Provides a method to represent the consensus across multiple runs of a clustering algorithm. Consensus Clustering is a methodology that determines the number of clusters in the data and assess the…

PFA
Desktop

PFA Pattern fusion analysis

Aligns local sample-patterns derived from each data type into a global…

Aligns local sample-patterns derived from each data type into a global sample-pattern to characterize phenotypes. PFA is a computational framework and a data-driven integration approach. Firstly, it…

MVDA
Desktop

MVDA Multi View genomic DAta

A multi-view genomic data integration framework. MVDA combines different types…

A multi-view genomic data integration framework. MVDA combines different types of measurements (such as mRNA expression, miRNA expression, DNA methylation, clinical data, etc) for a given set of…

ACE-it
Desktop

ACE-it Array CGH Expression integration tool

Helps to detect genes whose expression is affected by gene dosage within a…

Helps to detect genes whose expression is affected by gene dosage within a series of samples. ACE-it is a statistical tool that allows a user-defined cut-off for contaminating samples within the…

CHESS
Desktop

CHESS CgHExpreSS

A user-friendly tool for investigating disease specific genomic alterations and…

A user-friendly tool for investigating disease specific genomic alterations and quantitative relationships between those genomic alterations and genome-wide gene expression profiling. CHESS allows…

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