InfiniumPurify 1.3.1 – Predicting Tumor Purity from Methylation Microarray data

InfiniumPurify 1.3.1

:: DESCRIPTION

InfiniumPurify is a simple but effective method to estimate purities from the DNA methylation 450k array data.

::DEVELOPER

Yufang Qin <yfqin at shou.edu.cn>

 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX
  • R

:: DOWNLOAD

 InfiniumPurify

:: MORE INFORMATION

Citation:

Qin Y, Feng H, Chen M, Wu H, Zheng X.
InfiniumPurify: An R package for estimating and accounting for tumor purity in cancer methylation research.
Genes Dis. 2018 Feb 21;5(1):43-45. doi: 10.1016/j.gendis.2018.02.003. PMID: 30258934; PMCID: PMC6147081.

Predicting tumor purity from methylation microarray data.
Zhang N, Wu HJ, Zhang W, Wang J, Wu H, Zheng X.
Bioinformatics. 2015 Jun 25. pii: btv370.

aRrayLasso – Network-based Approach to Microarray Interconversion

aRrayLasso

:: DESCRIPTION

aRrayLasso implements a set of five open-source R functions that allow the user to acquire data from public sources such as GEO, train a set of Lasso models on that data, and directly map one microarray platform to another. aRrayLasso significantly predicts expression levels with higher fidelity than technical replicates of the same RNA pool, demonstrating its utility in the integration of data sets from different platforms.

::DEVELOPER

Adam Brown

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R

:: DOWNLOAD

 aRrayLasso

:: MORE INFORMATION

Citation

aRrayLasso: a network-based approach to microarray interconversion.
Brown AS, Patel CJ.
Bioinformatics. 2015 Aug 17. pii: btv469.

BRB-ArrayTools 4.6.2 – Visualization & Analysis of DNA Microarray Gene Expression Data

BRB-ArrayTools 4.6.2

:: DESCRIPTION

BRB-ArrayTools is an integrated software package for the analysis of DNA microarray data.

BRB-ArrayTools contains utilities for processing expression data from multiple experiments, visualization of data, multidimensional scaling, clustering of genes and samples, and classification and prediction of samples. BRB-ArrayTools features drill-down linkage to NCBI databases using clone, GenBank, or UniGene identifiers, and drill-down linkage to the NetAffx database using Probeset ids.

::DEVELOPER

the Biometric Research Branch of the Division of Cancer Treatment & Diagnosis of the National Cancer Institute

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

BRB-ArrayTools

:: MORE INFORMATION

Citation

Analysis of gene expression data using BRB-ArrayTools.
Simon R, Lam A, Li MC, Ngan M, Menenzes S, Zhao Y.
Cancer Inform. 2007 Feb 4;3:11-7.

OOMPA 3.1.0 – Object-Oriented Microarray and Proteomic Analysis

OOMPA 3.1.0

:: DESCRIPTION

OOMPA is an object-oriented microarray and proteomics analysis library implemented in R using S4 classes and compatible with BioConductor.

OOMPA includes experimental versions of two new packages:

  • ArrayCube: builds on fundamental classes from BioConductor to define a structure that generalizes the MINiML format used at the Gene Expression Omnibus. The main enhancement over MINiML format is the inclusion of an annotated data frame containing sample characteristics. The package provides routines to convert an ArrayCube into either an AffyBatch or an RGList, as appropriate.
  • MINiML: reads files in the MINiML format, as downloaded from the Gene Expression Omnibus, and stores them in R as ArrayCubes.

::DEVELOPER

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 OOMPA

:: MORE INFORMATION

Citation

Development of a robust classifier for quality control of reverse-phase protein arrays.
Ju Z, Liu W, Roebuck PL, Siwak DR, Zhang N, Lu Y, Davies MA, Akbani R, Weinstein JN, Mills GB, Coombes KR.
Bioinformatics. 2014 Nov 6. pii: btu736.

SIBER: systematic identification of bimodally expressed genes using RNAseq data.
Tong P, Chen Y, Su X, Coombes KR.
Bioinformatics. 2013 Mar 1;29(5):605-13. doi: 10.1093/bioinformatics/bts713. Epub 2013 Jan 9

integIRTy: a method to identify genes altered in cancer by accounting for multiple mechanisms of regulation using item response theory.
Tong P, Coombes KR.
Bioinformatics. 2012 Nov 15;28(22):2861-9. doi: 10.1093/bioinformatics/bts561

Cancer Inform. 2009 Aug 5;7:199-216.
The bimodality index: a criterion for discovering and ranking bimodal signatures from cancer gene expression profiling data.
Wang J, Wen S, Symmans WF, Pusztai L, Coombes KR.

BATS 20080710 – Bayesian Analysis of Time Series Microarray experiments

BATS 20080710

:: DESCRIPTION

BATS is a new user friendly GUI software for Bayesian Analysis of Time Series microarray experiments. It implements a truly functional fully Bayesian approach which allows an user to automatically identify and estimate differentially expressed genes.

::DEVELOPER

BioinfoLab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • MatLab

:: DOWNLOAD

 BATS

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2008 Oct 6;9:415. doi: 10.1186/1471-2105-9-415.
BATS: a Bayesian user-friendly software for analyzing time series microarray experiments.
Angelini C1, Cutillo L, De Canditiis D, Mutarelli M, Pensky M.

KegArray 1.2.4 – Microarray Data Analysis & Cluster

KegArray 1.2.4

:: DESCRIPTION

KegArray is a Java application that provides an environment for analyzing both transcriptome data (gene expression profiles) and metabolome data (compound profiles). Tightly integrated with the KEGG database, KegArray enables you to easily map those data to KEGG resources including PATHWAY, BRITE and genome maps.

::DEVELOPER

Kanehisa Laboratories

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Java

:: DOWNLOAD

KegArray

:: MORE INFORMATION

Citation

Methods Mol Biol. 2012;802:19-39.
The KEGG databases and tools facilitating omics analysis: latest developments involving human diseases and pharmaceuticals.
Kotera M, Hirakawa M, Tokimatsu T, Goto S, Kanehisa M.

PAA 1.26.0 – Biomarker Discovery with Protein Microarrays

PAA 1.26.0

:: DESCRIPTION

The R/Bioconductor package PAA (Protein Array Analyzer) facilitates a flexible analysis of protein microarrays for biomarker discovery (esp., ProtoArrays).

::DEVELOPER

Medizinisches Proteom-Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • R/ BioConductor

:: DOWNLOAD

 PAA

:: MORE INFORMATION

Citation

PAA: An R/Bioconductor package for biomarker discovery with protein microarrays.
Turewicz M, Ahrens M, May C, Marcus K, Eisenacher M.
Bioinformatics. 2016 Jan 22. pii: btw037

Chipster v4 – Analysis software for Microarray and other High-throughput data

Chipster v4

:: DESCRIPTION

Chipster is a user-friendly analysis software for high-throughput data. It contains over 280 analysis tools for next generation sequencing (NGS), microarray and proteomics data.

::DEVELOPER

CSC — IT Center for Science Ltd

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Java

:: DOWNLOAD

  Chipster

:: MORE INFORMATION

Citation

BMC Genomics. 2011 Oct 14;12:507. doi: 10.1186/1471-2164-12-507.
Chipster: user-friendly analysis software for microarray and other high-throughput data.
Kallio MA, Tuimala JT, Hupponen T, Klemelä P, Gentile M, Scheinin I, Koski M, Käki J, Korpelainen EI.

MENT – Microarray comprEssiOn Tools

MENT

:: DESCRIPTION

MENT is a set of tools for lossless compression of microarray images, however, it can be used in other kind of images such as medical, RNAi, etc.

::DEVELOPER

UA.PT Bioinformatics

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux / WIndows/ MacOsX
  • C Compiler

:: DOWNLOAD

 MENT

:: MORE INFORMATION

Citation

Luís M. O. Matos, António J. R. Neves, Armando J. Pinho,
“Lossy-to-lossless compression of biomedical images based on image decomposition”,
in Digital Signal Processing, (chapter proposal accepted on December 4, 2014).

GeneCommittee – Testing the Discriminatory Power of Gene Sets in Microarray data Classification

GeneCommittee

:: DESCRIPTION

GeneCommittee is a web-based interactive tool for giving specific support to the study of the discriminative classification power of custom hypothesis in the form of biological relevant gene sets.

::DEVELOPER

Sistemas Informáticos de Nueva Generación, UA.PT Bioinformatics

:: SCREENSHOTS

 N/A

::REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Jan 30;15:31. doi: 10.1186/1471-2105-15-31.
geneCommittee: a web-based tool for extensively testing the discriminatory power of biologically relevant gene sets in microarray data classification.
Reboiro-Jato M, Arrais JP, Oliveira JL, Fdez-Riverola F1