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http://bioconductor.org/packages/2.1/bioc/html/arrayMagic.html

Software providing a collection of utilities for quality control and processing of two-colour cDNA microarray data

Proper citation: arrayMagic (RRID:SCR_010933) Copy   

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https://www.bannerhealth.com/locations/sun-city/banner-sun-health-research-institute-santa-fe?y_source=1_MTE5MDcyOTgtNzE1LWxvY2F0aW9uLmdvb2dsZV93ZWJzaXRlX292ZXJyaWRl

Research institute for basic and translational research, clinical care, prevention and education in age-related conditions such as Alzheimer's and Parkinson's diseases, arthritis and cancer. Founded as a private, nonprofit biomedical research center, they now have nearly 100 international scientists and research staff. Their research programs have had significant impact on how physicians diagnose and treat diseases such as Alzheimer's, Parkinson's and arthritis. Sun Health is also internationally recognized for research on inflammation damage to brain tissue and how that affects Alzheimer's disease. They are one of just 31 national Alzheimer's Disease Core Centers in the nation. The Institute maintains collaborations with nationally-recognized institutions such as Johns Hopkins, Boston University and the University of Washington. In 2007, the institute opened a new research facility that allowed them to expand into areas such as orthopedics and fibromyalgia.

Proper citation: Banner Sun Health Research Institute (RRID:SCR_011110) Copy   

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http://www.baylorhealth.edu/Research/BRI/

Proper citation: Baylor Research Institute; Texas; USA (RRID:SCR_011113) Copy   

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http://smithlab.usc.edu/plone/software/piranha

A peak-caller for CLIP- and RIP-Seq data. It takes input in BED or BAM format and identifies regions of significant read enrichment. Additional covariates may optionally be provided to further inform the peak-calling process., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Piranha (RRID:SCR_010903) Copy   

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http://methmarker.mpi-inf.mpg.de/

Tool that facilitates the design and optimization of gene-specific DNA methylation assays. Beyond its use as an epigenetic primer-design tool, it provides extensive support for epigenetic biomarker optimization. Download MethMarker or start it directly from within your web browser.

Proper citation: MethMarker (RRID:SCR_010908) Copy   

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http://casp.rnet.missouri.edu/soydb/

A Knowledge Database of Soybean Transcription Factors. PSI-BLAST is available to find hits from the database.

Proper citation: SoyDB (RRID:SCR_010900) Copy   

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http://ppseq.sourceforge.net/

A software suite including a scalable hierarchical multitasking parallel infrastructure and the classical sequencing algorithms.

Proper citation: PPSEQ (RRID:SCR_010913) Copy   

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http://adacgh.bioinfo.cnio.es/

A web tool for the analysis of aCGH data sets. They focus on calling gains and losses and estimating the number of copy changes. Note: ADaCGH will continue being maintained, but is deprecated. Their new tool for CGH and CNV is WaviCGH, http://wavi.bioinfo.cnio.es/

Proper citation: ADaCGH (RRID:SCR_010916) Copy   

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http://www.genomics.agilent.com/en/product.jsp?cid=AG-PT-111&tabId=AG-PR-1017&_requestid=587725

Software for a complete CGH and CGH+SNP microarray data analysis and data reporting solution to streamline the day-to-day cytogenetic sample analysis research workflow.

Proper citation: Agilent CytoGenomics software (RRID:SCR_010917) Copy   

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http://aroma-project.org/

An R package for analyzing large Affymetrix data sets.

Proper citation: Aroma.affymetrix (RRID:SCR_010919) Copy   

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https://code.google.com/p/balony/

Image analysis and data inspection software for agar plates generated in high-throughput yeast genetics and genomics experiments.

Proper citation: balony (RRID:SCR_010968) Copy   

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http://carnegiescience.edu/

Andrew Carnegie founded the Carnegie Institution of Washington in 1902 as an organization for scientific discovery. His intention was for institution to be home to exceptional individualsmen and women with imagination and extraordinary dedication capable of working at the cutting edge of their fields. Today, Carnegie scientists work in six scientific departments on the West and East Coasts. Carnegie investigators are leaders in the fields of plant biology, developmental biology, Earth and planetary sciences, astronomy, and global ecology. They seek answers to questions about the structure of the universe, the formation of our solar system and other planetary systems, the behavior and transformation of matter when subjected to extreme conditions, the origin of life, the function of genes, and the development of organisms from single-celled egg to adult. The Carnegie Institution for Science is headquartered in Washington, D.C. It is an endowed, independent, nonprofit institution. Significant additional support comes from federal grants and private donations. A board of trustees, consisting of leaders in business, the sciences, education, and public service, oversees Carnegie''s operations. Each of the six departments has its own scientific director who manages day-to-day operations under the leadership of Richard A. Meserve, Carnegie president. In addition to the scientists on staff, there is a constantly changing roster of pre- and postdoctoral fellows and associates, as well as visiting investigators, at each facility. Each of the six departments is independently managed by a director, who is aided by support staff. Carnegie is also involved in education at the lower levels.

Proper citation: Carnegie Institution for Science (RRID:SCR_011137) Copy   

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http://www.bioinformatics.org/oligofaktory/

A free software for Mac OS X which designs long oligos for DNA microarrays, primers for PCR, siRNAs, and more��

Proper citation: OligoFaktory (RRID:SCR_010962) Copy   

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http://www.cmu.edu/

Carnegie Mellon University is a private nonprofit research university based in Pittsburgh, Pennsylvania. Founded in 1900 by Andrew Carnegie as the Carnegie Technical Schools, the university became the Carnegie Institute of Technology in 1912 and began granting four-year degrees.

Proper citation: Carnegie Mellon University; Pennsylvania; USA (RRID:SCR_011138) Copy   

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http://www.case.edu/

Private research university in Cleveland, Ohio.

Proper citation: Case Western Reserve University; Ohio; USA (RRID:SCR_011139) Copy   

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http://probemaker.sourceforge.net/

A Java software aimed at providing a framework for design and analysis of sets of oligonucleotide probes for use in multiplex assays for nucleic acid analyses and other purposes.

Proper citation: ProbeMaker (RRID:SCR_010964) Copy   

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https://www.panavation.com/

U.S. based consulting firm with wet-lab facilities and access to world-class analytic equipment. Areas of expertise include petroleum chemistry, alternative fuels, polymer chemistry, materials chemistry, high throughput reactions screening analytics.

Proper citation: Panavation (RRID:SCR_011019) Copy   

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http://probemer.cs.loyola.edu

THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 1, 2014, A web-based software tool that enables selecting optimal oligos for PCR applications and multiplex detection.

Proper citation: PROBEmer (RRID:SCR_010965) Copy   

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http://www.uhnresearch.ca/labs/tillier/ProDesign/ProDesign.html

Webserver that can be used to find oligonucleotide probe sets for microarray slides. The probes can be for individual sequences or for clusters of genes. This webserver accepts files up to 200 kb in size in order to minimize the running time. For larger files please download the program.

Proper citation: ProDesign (RRID:SCR_010966) Copy   

•   Source: SciCrunch Registry
  

http://www20.gencat.cat/portal/site/salut

Proper citation: Catalan Ministry of Health (RRID:SCR_011140) Copy   

•   Source: SciCrunch Registry