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http://www.bioconductor.org/packages/devel/bioc/html/VegaMC.html

Software package that enables the detection of driver chromosomal imbalances including loss of heterozygosity (LOH) from array comparative genomic hybridization (aCGH) data. It performs a joint segmentation of a dataset and uses a statistical framework to distinguish between driver and passenger mutation. VegaMC has been implemented so that it can be immediately integrated with the output produced by PennCNV tool. In addition, it produces in output two web pages that allows a rapid navigation between both the detected regions and the altered genes. In the web page that summarizes the altered genes, the link to the respective Ensembl gene web page is reported.

Proper citation: VegaMC (RRID:SCR_001267) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.1/bioc/html/VanillaICE.html

Software package using Hidden Markov Models for characterizing chromosomal alterations in high throughput SNP arrays.

Proper citation: VanillaICE (RRID:SCR_001268) Copy   

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http://sourceforge.net/projects/mutascope/

Software suite to analyze data from high throughput sequencing of PCR amplicons, with an emphasis on normal-tumor comparison for the accurate and sensitive identification of low prevalence mutations.

Proper citation: Mutascope (RRID:SCR_001265) Copy   

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http://www.wpic.pitt.edu/wpiccompgen/GemTools/GemTools.htm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software tools for modeling genetic ancestry based on the single nucleotide polymorphism (SNP) information. This package of functions helps the user account for genetic ancestry of a large number of individuals using spectral graph theory and projections to break a large problem into smaller pieces and calculate genetic ancestry information efficiently, i.e., a divide and conquer (dac) strategy. It is completely written in R and runs on any platform that supports R.

Proper citation: GemTools (RRID:SCR_001259) Copy   

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http://www.bioconductor.org/packages/release/bioc/html/SCAN.UPC.html

A microarray normalization software (SCAN) to facilitate personalized-medicine workflows with an extension (UPC) that estimates whether a given gene/transcript is active above background levels in a given sample. Rather than processing microarray samples as groups, which can introduce biases and present logistical challenges, SCAN normalizes each sample individually by modeling and removing probe- and array-specific background noise using only data from within each array. SCAN can be applied to one-channel (e.g., Affymetrix) or two-channel (e.g., Agilent) microarrays. The UPC method can be applied to one-channel or two-channel microarrays as well as to RNA-Seq read counts. Because UPC values are represented on the same scale and have an identical interpretation for each platform, they can be used for cross-platform data integration. A

Proper citation: SCAN.UPC (RRID:SCR_001334) Copy   

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http://neuroinformatics.kiv.zcu.cz/articles/read/eegerp-portal-eegbase-_2014-12-19

EEG base is a system for storage and management of EEG/ERP resources - data, metadata, tools and materials related to EEG/ERP experiments. EEG base advances electrophysiology research by enabling access to public data, tools and results of research groups. The system essentially offers the following set of features (the set of accessible features depends on a specific user role): * User authentication * Storage, update, and download of EEG/ERP data and metadata * Storage, update and download of EEG/ERP experimental design (experimental scenarios) * Storage, update and download of data related to testing subjects * Fulltext search * Sharing of knowledge and working in groups The system is based on tree layer architecture (MVC pattern) consisting of persistent layer (relational database), application layer (object oriented code, object relational mapping from persistence layer) and presentation layer (JSP). The persistence layer uses Hibernate framework; Oracle 11g database server is used to ensure the processing of large data files. Application and presentation layers are designed and implemented using Spring technology. This framework supports MVC architecture, Dependency injection and Aspect Oriented Programming. There were no significant difficulties with integration of both frameworks, Hibernate and Spring MVC. Spring Security framework is used to ensure management of authentication and user roles. Since the system is thought to be finally open to the whole EEG/ERP community it is necessary to protect EEG/ERP data and metadata, and especially personal data of testing subjects stored in the database from an unauthorized access. Then a restricted user policy is applied and user roles are introduced. The complete overview of the system features and user roles (use case diagram) is available in (Pergler 2009). Concerning the architectural layers there is a question which layer is more feasible for mapping of its structure into ontology. Currently we have studied two possibilities: * Mapping from the persistence layer (relational database) * Mapping from the application layer (object oriented code) The mapping from the application layer to an ontology includes the precedent object relational mapping provided by Hibernate framework.

Proper citation: EEGbase (RRID:SCR_001452) Copy   

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https://rdrr.io/bioc/betr/man/betr.html#heading-0

Software package that implements the Bayesian Estimation of Temporal Regulation algorithm to identify differentially expressed genes in microarray time-course data.

Proper citation: betr (RRID:SCR_001332) Copy   

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https://school.wakehealth.edu/departments/neurology

Department at the Wake Forest University's School of Medicine that hosts physicians who specialize in neurological topics such as neuromuscular disease, epilepsy, pediatric neurology, strokes, neuropsychology, neurosonology, and neurorehabilitaiton.

Proper citation: Wake Forest University School of Medicine: Department of Neurology (RRID:SCR_001453) Copy   

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http://www.roche.com/

A Swiss global health-care company that operates under two divisions: Pharmaceuticals and Diagnostics.

Proper citation: Roche (RRID:SCR_001326) Copy   

•   Source: SciCrunch Registry

http://www.sp.se/en/units/sppd/

A national research institute focusing on chemical, biochemical and pharmaceutical process development. Their main task is to build, use and provide expertise to increase success rates for academic and industrial actors with the development of new products and production processes. The institute forms an important resource and competence platform for knowledge generation, knowledge transfer, concept testing and risk sharing. Via SP Process Development, researchers and small and medium- sized enterprises (SMEs ) are provided access to tools, technology, equipment and complementing specialist knowledge. Sections that constitute the institute: * Analysis and Solid State * Catalysis * Process Development and Crystallization * Substance and Formulation What they do * Bringing together academia and industry to solve challenges within chemical, biochemical, technical and medical applications * Helping SMEs and academic research groups to drive ideas from the laboratory to commercial application * Enabling companies from different industries to increase collaboration regarding mutual challenges * Communicating challenges and requirements from industry to academic research groups

Proper citation: SP Process Development; Sodermanland; Sweden (RRID:SCR_011536) Copy   

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http://english.hi.is/

Public research university in Reykjavík, Iceland and the country's oldest and largest institution of higher education.

Proper citation: University of Iceland; Reykjavik; Iceland (RRID:SCR_011657) Copy   

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http://med.stanford.edu/

Medical school of Stanford University and is located in Stanford, California. It traces its roots to the Medical Department of the University of the Pacific, founded in San Francisco in 1858.

Proper citation: Stanford University School of Medicine; California; USA (RRID:SCR_011539) Copy   

•   Source: SciCrunch Registry

http://www.uic.edu/

Public research university in Chicago, Illinois. Its campus is in the Near West Side community area, adjacent to the Chicago Loop.

Proper citation: University of Illinois at Chicago; Illinois; USA (RRID:SCR_011660) Copy   

•   Source: SciCrunch Registry

http://www.sun.ac.za/english

Public research university situated in Stellenbosch, a town in the Western Cape province of South Africa.

Proper citation: Stellenbosch University; Western Cape; South Africa (RRID:SCR_011541) Copy   

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http://www.umd.edu/

Public research university in College Park, Maryland. Founded in 1856, UMD is the flagship institution of the University System of Maryland.

Proper citation: University of Maryland; Maryland; USA (RRID:SCR_011662) Copy   

•   Source: SciCrunch Registry

http://www.sll.se/sll/templates/NormalPage.aspx?id=19

The County Council is responsible for all publicly-financed healthcare and public transport in Stockholm County. The County Council is also responsible for other overall issues within the county, such as regional planning and cultural subsidies. Sweden''s political system has three democratically elected levels. At national level there is Parliament and the Government, at regional level there are county councils/regions, and at local level there are municipalities. The state decides on the laws and regulations that govern the work of county councils/regions and municipalities. healthcare, public transport and regional development the County Council''s broad responsibility

Proper citation: Stockholm County Council (RRID:SCR_011542) Copy   

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http://www.sussex.ac.uk/

A leading research-intensive university close to Brighton in the UK.

Proper citation: University of Sussex; Brighton; United Kingdom (RRID:SCR_011707) Copy   

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http://www.stonybrook.edu/

Public sea grant and space grant research university in Stony Brook, New York. It is one of four university centers of the State University of New York system.

Proper citation: Stony Brook University; New York; USA (RRID:SCR_011545) Copy   

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http://www.miami.edu/

Private research university in Coral Gables, Florida.

Proper citation: University of Miami; Florida; USA (RRID:SCR_011666) Copy   

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http://www.sgul.ac.uk/

A specialist medical and health sciences college and part of the University of London.

Proper citation: St Georges University of London; London; United Kingdom (RRID:SCR_011547) Copy   

•   Source: SciCrunch Registry