GeneTrail / GeneTrailExpress – Gene Set Analysis tool / for pre-processing Microarray data

GeneTrail / GeneTrailExpress

:: DESCRIPTION

GeneTrail is a comprehensive and efficient gene set analysis tool that offers a rich functionality and is easy to use.

GeneTrailExpress provides comprehensive normalization and scoring functions for pre-processing microarray data. The processed data is directly passed to GeneTrail for statistical evaluation in an extensive gene set analysis.

::DEVELOPER

Chair for clinical bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2008 Dec 22;9:552. doi: 10.1186/1471-2105-9-552.
GeneTrailExpress: a web-based pipeline for the statistical evaluation of microarray experiments.
Keller A1, Backes C, Al-Awadhi M, Gerasch A, Küntzer J, Kohlbacher O, Kaufmann M, Lenhof HP.

Backes C, Keller A, Kuentzer J, Kneissl B, Comtesse N, Elnakady YA, Müller R, Meese E, Lenhof HP.
GeneTrail–advanced gene set enrichment analysis.
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W186-92.

Genesis 1.7.7 / GenesisServer 1.1.0 – Cluster Analysis of Microarray data

Genesis 1.7.7 / GenesisServer 1.1.0

:: DESCRIPTION

Genesis integrates various tools for microarray data analysis such as filters, normalization and visualization tools, distance measures as well as common clustering algorithms including hierarchical clustering, self-organizing maps, k-means, principal component analysis, and support vector machines.

Genesis Server is an application server for computation of Hierarchical Clustering, Self Organizing Maps (SOM), k-means Clustering and Support Vector Machines (SVM).

::DEVELOPER

Genomics & Bioinformatics Graz, Graz University of Technology

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 Genesis , GenesisServer

:: MORE INFORMATION

Citation

Sturn A, Quackenbush J, Trajanoski Z.
Genesis: Cluster analysis of microarray data.
Bioinformatics. 2002 Jan;18(1):207-8.

Sturn A, Mlecnik B, Pieler R, Rainer J, Truskaller T, Trajanoski Z.
Client-Server environment for high-performance gene expression data analysis.
Bioinformatics. 19: 772-773 (2003)

GENECLUST 1.0.2 – Exploratory Analysis of Gene Expression Microarray data

GENECLUST 1.0.2

:: DESCRIPTION

GeneClust is a piece of computer software which can be used as a tool for exploratory analysis of gene expression microarray data. The development of GeneClust was motivated by surging interest to search for interpretable biological structure in gene expression microarray data.

::DEVELOPER

Kim-Anh Do, Ph.D.

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 GENECLUST

:: MORE INFORMATION

Citation

Cancer Inform. 2007;5:25-43. Epub 2007 Apr 2.
Application of gene shaving and mixture models to cluster microarray gene expression data.
Do KA, McLachlan GJ, Bean R, Wen S.

CALIB 1.34.0 – Estimate absolute Expression levels from two color Microarray data

CALIB 1.34.0

:: DESCRIPTION

CALIB (Calibration model) is a BioConductor package for estimating absolute expression levels from two color microarray data

::DEVELOPER

Bioinformatics Research Group, Belgium

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 CALIB

:: MORE INFORMATION

Citation

CALIB: a Bioconductor package for estimating absolute expression levels from two-color microarray data.
Zhao H, Engelen K, De Moor B, Marchal K.
Bioinformatics. 2007 Jul 1;23(13):1700-1. Epub 2007 May 7.

PeakFinder 1.0 – Find Cohesin Binding Sites in Yeast ChIP Microarray Data

PeakFinder 1.0

:: DESCRIPTION

PeakFinder program was developed to find cohesin binding sites represented by the peaks in yeast chromatin immunoprecipitation (ChIP) microarray data, but can be applied to plot any measurement against a parameter such as genome coordinate, to interactively analyze the measurement plot, and to annotate the peaks on the basis of local properties of the curve.

::DEVELOPER

Earl F. Glynn

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

PeakFinder

:: MORE INFORMATION

Citation

Glynn EF, Megee PC, Yu H-G, Mistrot C, Unal E, et al. (2004)
Genome-wide mapping of the cohesin complex in the yeast Saccharomyces cerevisiae.
PLoS Biol 2(9): e259. doi:10.1371/journal.pbio.0020259

CpGassoc 2.11 – Analysis of DNA Methylation Microarray data

CpGassoc 2.11

:: DESCRIPTION

CpGassoc – An R Function for Analysis of DNA Methylation Microarray Data The analysis of DNA methylation data has recently garnered attention among researchers from a variety of backgrounds, due to the availability of high-throughput methylation microarrays. The number of CpG sites that can be analyzed is growing rapidly – for example, the latest Illumina Infinium BeadChip interrogates ~450,000 CpG sites. With the growing interest in DNA methylation and the growing volume of data analyzed, there is a need for software to perform these types of analyses.

::DEVELOPER

Department of Human Genetics, Emory University School of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

CpGassoc

:: MORE INFORMATION

Citation

R. T. Barfield et al.
CpGassoc – An R Function for Analysis of DNA Methylation Microarray Data.
American Society of Human Genetics/ICHG 2011

MethLAB 1.5 – Analysis of DNA Methylation Microarray data

MethLAB 1.5

:: DESCRIPTION

MethLAB provides a graphical user interface (GUI) to facilitate analysis of DNA methylation microarray data, allowing users with no experience using statistical software to implement flexible and powerful analyses of array-based DNA methylation data.

::DEVELOPER

Department of Human Genetics, Emory University School of Medicine

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

MethLAB

:: MORE INFORMATION

Citation

Varun Kilaru, Richard T. Barfield, James W. Schroeder, Alicia K. Smith, Karen N. Conneely.
MethLAB: A GUIpackage for the analysis of array-based DNA methylation data (2012).
Epigenetics, Volume 7, Issue 3

SVA 3.14.0 – Surrogate Variable Analysis

SVA 3.14.0

:: DESCRIPTION

The sva package contains functions for removing batch effects and other unwanted variation in high-throughput experiment.

::DEVELOPER

SVA team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 sva

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Mar 15;28(6):882-3. doi: 10.1093/bioinformatics/bts034. Epub 2012 Jan 17.
The sva package for removing batch effects and other unwanted variation in high-throughput experiments.
Leek JT1, Johnson WE, Parker HS, Jaffe AE, Storey JD.

Johnson, WE, Rabinovic, A, and Li, C (2007).
Adjusting batch effects in microarray expression data using Empirical Bayes methods.
Biostatistics 8(1):118-127.

MicroPreP – Microarray data Preprocessing framework

MicroPreP

:: DESCRIPTION

MicroPreP framework was developed to provide a pipeline to transform raw intensity data from cDNA microarrays into high-quality data

::DEVELOPER

Anne de Jong

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 MicroPreP

:: MORE INFORMATION

Citation

Appl Bioinformatics. 2003;2(4):241-4.
MicroPreP: a cDNA microarray data pre-processing framework.
van Hijum SA, García de la Nava J, Trelles O, Kok J, Kuipers OP.

PageMan 0.12 – Annotates, Investigates, and Condenses Microarray data in the Context of Functional Ontologies

PageMan 0.12

:: DESCRIPTION

PageMan is a tool to get a quick overview of multiparallel experiments. PageMan also helps comparing experiments from different organisms.

::DEVELOPER

Max Planck Institute for Molecular Plant Physiology, Golm, Germany.

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 PageMan

:: MORE INFORMATION

Citation

Usadel B, Nagel A, Steinhauser D, Gibon Y, Blaesing OE, Redestig H, Sreenivasulu N, Krall L, Hannah MA, Poree F, Fernie AR, Stitt M (2006)
PageMan an interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments,
BMC Bioinformatics 18:7:535