Tag: Integrative Analysis

MIA – Matrix Integrative Analysis

MIA

:: DESCRIPTION

MIA is a MATLAB package, implementing and extending four computational methods (Guide). MIA can integrate diverse types of genomic data (e.g., copy number variation, DNA methylation, gene expression, microRNA expression profiles and/or gene network data) to identify the underlying modular patterns. MIA is flexible and can handle a wide range of biological problems and data types.

::DEVELOPER

Shihua Zhang’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • MatLab

:: DOWNLOAD

MIA

:: MORE INFORMATION

Citation

Chen J, Zhang S.
Matrix Integrative Analysis (MIA) of Multiple Genomic Data for Modular Patterns.
Front Genet. 2018 May 29;9:194. doi: 10.3389/fgene.2018.00194. PMID: 29910825; PMCID: PMC5992392.

HiChIP – A high-throughput pipeline for Integrative Analysis of ChIP-Seq data

HiChIP

:: DESCRIPTION

HiChIP pipeline is designed for performing comprehensive analysis of chromatin immunoprecipitation and sequencing (ChIP-Seq) data.

::DEVELOPER

Bioinformatics Program, Division of Biomedical Statistics and Informatics, Mayo Clinic Research

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / VirtualBox

:: DOWNLOAD

 HiChIP

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Aug 15;15:280. doi: 10.1186/1471-2105-15-280.
HiChIP: a high-throughput pipeline for integrative analysis of ChIP-Seq data.
Yan H, Evans J, Kalmbach M, Moore R, Middha S, Luban S, Wang L, Bhagwate A, Li Y, Sun Z, Chen X, Kocher JP

Correlate 1.03 – Integrative Analysis of 2 Genomic Data Sets

Correlate 1.03

:: DESCRIPTION

Correlate is an Excel plug-in for performing an integrative analysis of two genomic data sets.

If two sets of assays (e.g. gene expression and DNA copy number) have been performed on the same set of patient samples then sparse CCA can be used to find a set of variables in assay 1 that is maximally correlated with a set of variables in assay 2.

::DEVELOPER

Sam Gross / Balasubramanian Narasimhan / Robert Tibshirani /Daniela Witten

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

Correlate

:: MORE INFORMATION

paper: Witten DM, Tibshirani R, and T Hastie (2009) A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis. Biostatistics 10(3): 515-534