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http://www.biostat.wisc.edu/~kendzior/EBSEQ/
Software R package for RNA-Seq Differential Expression Analysis.
Proper citation: EBSeq (RRID:SCR_003526) Copy
http://www.hsph.harvard.edu/skat/metaskat/
A R package for multiple marker meta-analysis.
Proper citation: MetaSKAT (RRID:SCR_003489) Copy
http://genomesavant.com/p/home/index
A next-generation genome browser software designed for the latest generation of genome data.
Proper citation: Savant (RRID:SCR_003488) Copy
https://code.google.com/p/mztab/
A Java interface to the mzTab data exchange format for reporting a summary of proteomics results.
Proper citation: jmzTab (RRID:SCR_003481) Copy
http://www.broadinstitute.org/mpg/magenta/
A computational tool that tests for enrichment of genetic associations in predefined biological processes or sets of functionally related genes, using genome-wide genetic data as input.
Proper citation: MAGENTA (RRID:SCR_003422) Copy
http://cran.r-project.org/web/packages/NAPPA/
Software that enables the processing and normalization of the standard mRNA data output from the Nanostring nCounter software.
Proper citation: NAPPA (RRID:SCR_003419) Copy
https://code.google.com/p/fade/
A software package designed to determine the methylation parameter at each cytosine or cytosine-guanine position in the human genome. FadE uses color reads produced by the SOLiD sequencer or nucleotide reads produced by the Illumina or 454 sequencing platforms.
Proper citation: FadE (RRID:SCR_003448) Copy
https://code.google.com/p/proteomecommons-tranche/
A distributed file storage system that you can upload files to and download files from. All files uploaded to the repository are replicated several times to protect against their accidental loss. Files uploaded to the repository can be of any size, can be of any file type, and can be encrypted with a passphrase of your choosing. The Proteome Commons Tranche repository is the first instance of a Tranche repository. Tranche, was created so that anybody can take it and make their own Tranche repository. This is the first implementation of the Tranche software, and is useful as a test bed for the software. This repository relies on educational institutions to provide the hardware and facilities for Tranche servers. While we maintain a set of servers, the continued growth of this public resource will rely on the generosity of the institutions that use the repository most.
Proper citation: Proteome Commons Tranche repository (RRID:SCR_003441) Copy
http://www.compgen.org/tools/metagen
Software program providing a method for meta-analysis of case-control genetic association studies using random-effects logistic regression.
Proper citation: metagen (RRID:SCR_003443) Copy
Initiative to improve health by speeding up the development of, and patient access to, innovative medicines, particularly in areas where there is an unmet medical or social need. It does this by initiating and managing consortia composed of the key players involved in healthcare research, including universities, the pharmaceutical and other industries, small and medium-sized enterprises (SMEs), patient organizations, and medicines regulators. IMI is a public-private partnership between the European Union and the European pharmaceutical industry, represented by the European Federation of Pharmaceutical Industries and Associations (EFPIA), with a timeframe separated into two phases (2008-2013, 2014-2024) that are each defined by unique research agendas. The first phase (2008 2013) had four pillars that defined the focus of its research agenda: * Predicting safety: evaluating the safety of a compound during the pre-clinical phase of the development process and the later phases in clinical development. * Predicting efficacy: improving the ability to predict how a drug will interact in humans and how it may produce a change in function. * Knowledge management: utilization of information and data for predicting safety and efficacy. * Education and training: closing existing training gaps in the drug development process. Some of the consortia managed under IMI focused on specific health issues while others focused on broader challenges in drug development. Additionally, IMI launched a number of education and training projects during its first phases. The goal of the second phase (IMI2, 2014-2024) is to develop next generation vaccines and drugs. The focus is on delivering the right prevention and treatment for the right patient at the right time. There is a strong focus on the development of new medicines with an emphasis on tools and methods that accelerate patient access to new medicines. IMI2's agenda can be defined by four axes of research: * target validation and biomarker research (efficacy and safety) * adoption of innovative clinical trial paradigms * innovative medicines * patient-tailored adherence programs As part of its distinct goals, IMI2 aims to deliver: * 30% better success rate in clinical trials of priority medicines identified by the WHO; clinical proof of concept in immunological, respiratory, neurological and neurodegenerative diseases in five years; * new and approved diagnostic markers for four of these diseases and at least two new medicines which could either be new antibiotics or new therapies for Alzheimer's disease.
Proper citation: Innovative Medicines Initiative (RRID:SCR_003754) Copy
A consortium that focuses their efforts on discovering and developing new pharmaceutical drugs, vaccines (both preventive and therapeutic) and diagnostics against the infectious diseases that are prevalent in developing countries. The initial targets are those disorders designated by WHO as neglected tropical diseases prevalent in developing nations. The consortium aims to facilitate international partnerships that enable Japanese technology, innovations, and insights to play a more direct role in improving global health. Another goal of GHIT is to develop a new drug-discovery screening platform to assist the screening of compound libraries housed within Japanese companies and academic institutions. The vision is to have Japanese research organizations donate compounds, with the Fund reimbursing screening costs and leveraging screening programs of existing product-development partners.
Proper citation: Global Health Innovative Technology Fund (RRID:SCR_003753) Copy
http://www.coca-colacompany.com/
An American multinational beverage corporation and manufacturer, retailer and marketer of nonalcoholic beverage concentrates and syrups, which is headquartered in Atlanta, Georgia. (Wikipedia) It is the world's largest beverage company, refreshing consumers with more than 500 sparkling and still brands.
Proper citation: Coca-Cola Company (RRID:SCR_003749) Copy
http://www.sevenhillsbioreagents.com/
An Antibody supplier
Proper citation: Seven Hills Bioreagents (RRID:SCR_003748) Copy
http://ims.cochrane.org/revman/about-revman-5
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023.A software package that does meta-analysis and provides results in tabular format and graphically.
Proper citation: RevMan (RRID:SCR_003581) Copy
An Antibody supplier
Proper citation: Torrey Pines Biolabs (RRID:SCR_003580) Copy
A not-for-profit research and development laboratory focused on the design, development, and deployment of advanced technological solutions for the nation's most challenging and important problems in security, space exploration, healthcare, and energy. Their expertise includes the areas of guidance, navigation, and control systems; fault-tolerant computing; advanced algorithms and software solutions; modeling and simulation; and MEMS and multichip module technology. With a strong commitment to delivering working solutions to their sponsors, they apply their expertise to a variety of domains, including autonomous air, land, sea, and space systems; information integration; distributed sensors and networks; precision-guided munitions; and biomedical engineering; chemical/biological defense; and energy system modeling and management. When appropriate for the needs of their sponsors, they will work with commercial partners to transition their technology to commercial production.
Proper citation: Charles Stark Draper Laboratory (RRID:SCR_003736) Copy
http://bioinformatics.bc.edu/marthlab/wiki/index.php/PyroBayes
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. A base caller for pyrosequences from the 454 Life Sciences sequencing machines.
Proper citation: PyroBayes (RRID:SCR_003757) Copy
Commercial organization developing a disruptive, proprietary technology platform for the direct, electronic analysis of single molecules. The instruments GridION and MinION are adaptable for the analysis of DNA, RNA, proteins, small molecules and other types of molecule. Consequently, the platform has a broad range of potential applications, including scientific research, personalized medicine, crop science and security / defence.
Proper citation: Oxford Nanopore Technologies (RRID:SCR_003756) Copy
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