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http://www.cos.uni-heidelberg.de/index.php/n.ha

Software for detecting Co-Occurrence and Spatial Arrangement of Transcription Factor Binding Motifs in Genome-Wide Datasets.

Proper citation: COPS (RRID:SCR_010852) Copy   

•   Source: SciCrunch Registry

http://www.illumina.com/software/genomestudio_software.ilmn

Visualize and analyze data generated by all of Illumina''s platforms.

Proper citation: GenomeStudio (RRID:SCR_010973) Copy   

•   Source: SciCrunch Registry

http://www.bu.edu/jlab/wp-assets/ComBat/Abstract.html

Adjusting batch effects in microarray expression data using Empirical Bayes methods.

Proper citation: ComBat (RRID:SCR_010974) Copy   

•   Source: SciCrunch Registry

http://www.bioinformatics.polimi.it/MicroGen/

Software application package for a Minimum Information About Microarray Experiments (MIAME) compliant web-based information system for managing all the information completely characterizing spotted microarray experiments and the produced data.

Proper citation: MicroGen (RRID:SCR_010976) Copy   

•   Source: SciCrunch Registry

http://woldlab.caltech.edu/wiki/RNASeq#Dual-use_E-RANGE

A Python package for doing RNA-seq and ChIP-seq (hence the dual-use).

Proper citation: E-RANGE (RRID:SCR_010856) Copy   

•   Source: SciCrunch Registry

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://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://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