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.

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.

ProfileChaser – Searching Microarray Repositories based on Genome-wide Patterns of differential Expression

ProfileChaser

:: DESCRIPTION

ProfileChaser searches the Gene Expression Omnibus for experiments whose differential expression looks similar to a query experiment.

::DEVELOPER

ProfileChaser team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • PHP

:: DOWNLOAD

 ProfileChaser

:: MORE INFORMATION

Citation

ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression.
Engreitz JM, Chen R, Morgan AA, Dudley JT, Mallelwar R, Butte AJ.
Bioinformatics. 2011 Dec 1;27(23):3317-8. doi: 10.1093/bioinformatics/btr548.

BRB-ArrayTools 4.5.0 b1 – Visualization & Analysis of DNA Microarray Gene Expression Data

BRB-ArrayTools 4.5.0 b1

:: 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.

BRB-ArrayTools can be used to analyze both single-channel and dual-channel experiments. The package is very portable and is not restricted to use with any particular array platform, scanners, image analysis software or database. The package is implemented as an Excel add-in so that it has an interface that is familiar to biologists.

The computations are performed by sophisticated and powerful analytics external to Excel but invisible to the user. The software was developed by statisticians experienced in the analysis of microarray data and involved in research on improved analysis tools. BRB-ArrayTools serves as a tool for instructing users on effective and valid methods for the analysis of their data. The existing suite of tools will be updated as new methods of analyses are being developed.

::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.

SAM 4.01 – Significance Analysis of Microarrays

SAM 4.01

:: DESCRIPTION

SAM (Significance Analysis of Microarrays) is a statistical technique for finding significant genes in a set of microarray experiments, a supervised learning software for genomic expression data mining.

The input to SAM is gene expression measurements from a set of microarray experiments, as well as a response variable from each experiment. The response variable may be a grouping like untreated, treated [either unpaired or paired], a multiclass grouping (like breast cancer, lymphoma, colon cancer, . . . ), a quantitative variable (like blood pressure) or a possibly censored survival time.

::DEVELOPER

Stanford University Statistics and Biochemistry Labs

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 SAM

:: MORE INFORMATION

Citation

Jun Li and Robert Tibshirani (2011)
Finding consistent patterns: a nonparametric approach for identifying differential expression in RNA-Seq data.
Stat Methods Med Res. 2011 Nov 28.

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.

InfiniumPurify – Predicting Tumor Purity from Methylation Microarray data

InfiniumPurify

:: DESCRIPTION

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

::DEVELOPER

Xiaoqi Zheng

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX
  • Python

:: DOWNLOAD

 InfiniumPurify

:: MORE INFORMATION

Citation:

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.

Primegens w3 – Primer Design for Microarray

Primegens w3

:: DESCRIPTION

Primegens ((PRIMEr Design Using GEN Specific Fragments) is a software for high-throughput primer and probe design. The program uses two third party executables like Primer3 and Megablast.

::DEVELOPER

Primegens Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows

:: DOWNLOAD

 Primegens

:: MORE INFORMATION

Citation

Gyan Prakash Srivastava, Juyuan Guo, Huidong Shi and Dong Xu.
PRIMEGENS-v2: genome-wide primer design for analyzing DNA methylation pattern of CpG island“.
Bioinformatics 2008 24(17):1837-42.

AffyRNADegradation 1.14.0 – Analyze and Correct Probe Positional Bias in Microarray data due to RNA Degradation

AffyRNADegradation 1.14.0

:: DESCRIPTION

AffyRNADegradation helps with the assessment and correction of RNA degradation effects in Affymetrix 3′ expression arrays.

::DEVELOPER

Mario Fasold <fasold at izbi.uni-leipzig.de>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX / Window
  • R
  • BioConductor

:: DOWNLOAD

 AffyRNADegradation

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jan 1;29(1):129-31. doi: 10.1093/bioinformatics/bts629. Epub 2012 Oct 24.
AffyRNADegradation: control and correction of RNA quality effects in GeneChip expression data.
Fasold M1, Binder H.

OLIN 1.46.0 – Optimized Normalization, Visualization and Quality Testing of two-channel Microarray data

OLIN 1.46.0

:: DESCRIPTION

OLIN (Optimised Local Intensity-dependent Normalisation) is the software developed for optimized normalization.

::DEVELOPER

Matthias E. Futschik

:: SCREENSHOTS

OLIN

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R package
  • BioConductor
  • R-TclTk

:: DOWNLOAD

 OLIN

:: MORE INFORMATION

Citation

Bioinformatics. 2005 Apr 15;21(8):1724-6.
OLIN: optimized normalization, visualization and quality testing of two-channel microarray data.
Futschik ME, Crompton T.