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

BioMedical Informatics Laboratory

:: 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.

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. PriceAdam 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.

RepeatMap – Determine RNA probes for in situ Hybridizations and Microarray experiments

RepeatMap

:: DESCRIPTION

RepeatMap is client/server pair of programs to determine very specific probes for in situ hybridizations and microarray experiments. The goal of the project is to provide highly specific RNA probes.

::DEVELOPER

Aaron Arvey

:: SCREENSHOTS

RepeatMap

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • Java

:: DOWNLOAD

 RepeatMap

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2010 Jun;38(10):e115. doi: 10.1093/nar/gkq042. Epub 2010 Feb 17.
Minimizing off-target signals in RNA fluorescent in situ hybridization.
Arvey A, Hermann A, Hsia CC, Ie E, Freund Y, McGinnis W.

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

José Caldas, firstname.lastname@aalto.fi.

:: 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

ResultViewer 1.0 – Browse the Data Analysis Results of Microarray Experiments

ResultViewer 1.0

:: DESCRIPTION

ResultViewer is an application that allows investigators to browse the data analysis results of their microarray experiments.

::DEVELOPER

ResultViewer Team

:: SCREENSHOTS

N/A

: REQUIREMENTS

  • Windows

:: DOWNLOAD

 ResultViewer

:: 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

:: 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.