OpWise – Operons Aid the Identification of differentially Expressed Genes in Bacterial Microarray Experiments

OpWise

:: DESCRIPTION

To estimate the reliability of bacterial microarray experiments, OpWise uses the agreement of measurements within operons to estimate the amount of systematic bias in the data. OpWise relies on the MicrobesOnline operons predictions.

::DEVELOPER

Morgan N. Price, Adam P. Arkin, and Eric J. Alm

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / Mac OsX
R package

:: DOWNLOAD

OpWise

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2006 Jan 13;7:19.
OpWise: operons aid the identification of differentially expressed genes in bacterial microarray experiments.
Price MN, Arkin AP, Alm EJ.

MicroGen – Web Server for Microarray Experiments

MicroGen

:: DESCRIPTION

MicroGen is MIAME compliant web-based information system for managing all the information completely characterizing spotted microarray experiments and the produced data. Based on experiment workflow, it supports distributed collaborative work in the production pipeline of spotted microarray experiments.

::DEVELOPER

Masseroli Marco, Ph.D

:: SCREENSHOTS

n/a

:: REQUIREMENTS

Windows
Access
Excel

:: DOWNLOAD

MicroGen

:: MORE INFORMATION

Citation

Burgarella S, Cattaneo D, Pinciroli F, Masseroli M.
MicroGen: a MIAME compliant Web system for microarray experiment information and workflow management.
BMC Bioinformatics 2005 Dec. 1; 6(Suppl 4): S6, p.1-6.

gseaLda – Probabilistic Retrieval and Visualization of Biologically Relevant Microarray Experiments

gseaLda

:: DESCRIPTION

gseaLda is a r package for probabilistic retrieval and visualization of biologically relevant microarray experiments

::DEVELOPER

Probabilistic Machine Learning

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows /MacOsX
R package

:: DOWNLOAD

gseaLda

:: MORE INFORMATION

Citation

Probabilistic retrieval and visualization of biologically relevant microarray experiments
José Caldas, Nils Gehlenborg, Ali Faisal, Alvis Brazma and Samuel Kaski
Bioinformatics (2009) 25 (12): i145-i153.

affyParaEBI 1.0.0 – Preprocessing of Microarray Experiments

affyParaEBI 1.0.0

:: DESCRIPTION

The affyParaEBI is an R based pipeline for parallel pre-processing of Affymetrix TM chips. The pipeline starts from a directory containing raw CEL files files and produces Bioconductor R objects containing gene expression measurements suitable for further analysis.

::DEVELOPER

EBI.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
R package
Bioconductor

:: DOWNLOAD

affyParaEBI

:: MORE INFORMATION

tRMA 1.0 – Modification of RMA to Normalize Microarray Experiments

tRMA 1.0

:: DESCRIPTION

tRMA is a modification of RMA to normalize microarray experiments for correlation-based analysis.

::DEVELOPER

Usadel Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/MacOsX
R package

:: DOWNLOAD

tRMA

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 Nov 11;11:553. doi: 10.1186/1471-2105-11-553.
Algorithm-driven artifacts in median Polish summarization of microarray data.
Giorgi FM, Bolger AM, Lohse M, Usadel B.

PubArray 1.0.0 – Turn Analyzed Results of Microarray Experiment into Web Application

PubArray 1.0.0

:: DESCRIPTION

PubArray is a desktop application that allows you to turn the analyzed results of your microarray experiment into a web application which is accessible via your browser.

::DEVELOPER

The Churchill Group

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / Mac OsX
java

:: DOWNLOAD

PubArray

:: MORE INFORMATION

MIAMExpress 7.5 – Submission Tool for Microarray Experiments

MIAMExpress 7.5

:: DESCRIPTION

MIAMExpress is a MIAME-compliant web-based tool for submitting microarray data and microarray designs to the ArrayExpress database. It is suitable for submitting both single-channel (e.g. Affymetrix) and 2-channel data.

::DEVELOPER

EBI ArrayExpress

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows / Mac OsX
JAVA
Perl

:: DOWNLOAD

MIAMExpress

:: MORE INFORMATION

Citation:

Parkinson et al. 2010 ArrayExpress update—an archive of microarray and high-throughput sequencing-based functional genomics experiments. Nucl. Acids Res., doi: 10.1093/nar/gkq1040. Pubmed ID 21071405.