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http://sourceforge.net/apps/mediawiki/vancouvershortr/index.php?title=FindPeaks

Software application that can be used for converting Eland, Maq (.map), BED or other files into WIG files and identifying areas of enrichment (ChIP-Seq analysis).

Proper citation: FindPeaks (RRID:SCR_010857) Copy   

•   Source: SciCrunch Registry

http://furlonglab.embl.de/methods/tools/coco

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 22, 2021.A computational tool that allows the user to search, visualise and store different data associated with gene expression.

Proper citation: CoCo (RRID:SCR_010947) Copy   

•   Source: SciCrunch Registry

http://bioinf.wehi.edu.au/limma/

Software package for the analysis of gene expression microarray data, especially the use of linear models for analyzing designed experiments and the assessment of differential expression.

Proper citation: LIMMA (RRID:SCR_010943) Copy   

•   Source: SciCrunch Registry

http://www-ps.informatik.uni-tuebingen.de/mayday/wp/

Software providing a workbench for visualization, analysis and storage of microarray data. It features a graphical user interface and supports the development and integration of existing and new analysis methods. Besides the infrastructural core functionality, Mayday offers a variety of plug-ins, such as various interactive viewers, a connection to the R statistical environment, a connection to SQL-based databases, and different clustering methods, including phylogenetic methods. In addition, so-called meta information objects are provided for annotation of the microarray data allowing integration of data from different sources. This meta information can be used to enhance visualizations, such as in the enhanced heatmap visualization. Written in the Java programming language, Mayday is extremely portable and runs on all platforms supporting the Java runtime environment 1.6.

Proper citation: Mayday (RRID:SCR_010945) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/RPPanalyzer/index.html

A statistical tool developed to read reverse-phase protein array data, to perform the basic data analysis and to visualize the resulting biological information.

Proper citation: RPPanalyzer (RRID:SCR_010959) Copy   

•   Source: SciCrunch Registry

http://www.webcitation.org/query.php?url=http://psychiatry.igm.jhmi.edu/kaminsky/software.htm&refdoi=10.1186/1471-2105-14-76

A Perl based tool for the identification of differentially enriched regions in tiling microarray data.

Proper citation: BioTile (RRID:SCR_010953) Copy   

•   Source: SciCrunch Registry

http://www.rforge.net/IMA/

A software package designed to automate the pipeline for analyzing site-level and region-level methylation changes in epigenetic studies utilizing the 450K DNA methylation microarray.

Proper citation: IMA (RRID:SCR_010955) Copy   

•   Source: SciCrunch Registry

http://www.cs.ubc.ca/~sshah/acgh/

A software for detection of DNA copy number alterations (CNAs) from array comparative genomic hybridization (aCGH) data.

Proper citation: CNA-HMMer (RRID:SCR_010924) Copy   

•   Source: SciCrunch Registry

http://www.zbh.uni-hamburg.de/?id=292

A web-based software tool for the integrative analysis of cancer genomics data. It stores different kinds of downstream processed data from multiple samples in a single database. A powerful search interface allows to dynamically filter the data to be displayed with respect to different criteria. The combination of AJAX technology and a fast visualization engine facilitates a highly dynamic visualization for large amounts of data. FISH Oracle 2 is able to simultaneously display different data sets, thus simplifying their comparison. Filter and display options can be changed on the fly. High quality image export enables the life scientist to easily communicate the results, e.g. in presentations or publications. A comprehensive data administration assures to keep track of the data stored in the database.

Proper citation: FISH Oracle (RRID:SCR_010927) Copy   

•   Source: SciCrunch Registry

http://opossum.cisreg.ca

A web-based system for the detection of over-represented conserved transcription factor binding sites and binding site combinations in sets of genes or sequences.

Proper citation: oPOSSUM (RRID:SCR_010884) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.bioengr.uic.edu/TFBSGroup/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. A Software program for Predicting Transcription Factor Binding Sites.

Proper citation: TFBSGroup (RRID:SCR_010887) Copy   

•   Source: SciCrunch Registry

http://www.softgenetics.com/CGHExplorer.html

An easy-to-use software tool for analyzing two color copy number alteration arrays from multiple platforms, including Agilent Technologies, Illumina, AffyMetrix, NimbleGen and others.

Proper citation: CGH Explorer (RRID:SCR_010920) Copy   

•   Source: SciCrunch Registry

http://owww.molgen.mpg.de/~abt_rop/molecular_cytogenetics/GenomeCAT.html

A software for the analysis and visualization of array CGH data.

Proper citation: CGHPRO (RRID:SCR_010921) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/cghseg/index.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. Software R package dedicated to the analysis of CGH profiles using segmentation models.

Proper citation: CGHseg (RRID:SCR_010922) Copy   

•   Source: SciCrunch Registry

http://liulab.dfci.harvard.edu/NPS/

A python software package that can identify nucleosome positions given histone-modification ChIP-seq or nucleosome sequencing at the nucleosome level.

Proper citation: NPS (RRID:SCR_010890) Copy   

•   Source: SciCrunch Registry

http://base.thep.lu.se/

A comprehensive management application for information, data, and analysis of microarray experiments, available as free open source software.

Proper citation: BASE (RRID:SCR_010937) Copy   

•   Source: SciCrunch Registry

http://linus.nci.nih.gov/BRB-ArrayTools.html

An integrated software package for the visualization and statistical analysis of DNA microarray gene expression data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: BRB-ArrayTools (RRID:SCR_010938) Copy   

•   Source: SciCrunch Registry

http://mmb.pcb.ub.es/nucleR/

A R/Bioconductor package for a flexible and fast recognition of nucleosome positioning from next generation sequencing and tiling arrays experiments. The software is integrated with standard high-throughput genomics R packages and allows for in situ visualization as well as to export results to common genome browser formats.

Proper citation: nucleR (RRID:SCR_010895) Copy   

•   Source: SciCrunch Registry

http://genovar.sourceforge.net/

A Detection and Visualization software tool for Genomic Variants.

Proper citation: Genovar (RRID:SCR_010930) Copy   

•   Source: SciCrunch Registry

http://www.arrayanalysis.org/

Tools for microarray quality control and pre-processing.

Proper citation: ArrayAnalysis.org (RRID:SCR_010932) Copy   

•   Source: SciCrunch Registry