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https://github.com/brantp/rtd

Reference-free ddRADseq analysis software tools. The pipeline script generates reference-sorted, indexed BAM from uniqued reads from radtag sequencing lanes.

Proper citation: rtd (RRID:SCR_000337) Copy   

•   Source: SciCrunch Registry

http://www.cdisc.org/

A global, open, multidisciplinary, non-profit organization that has established standards to support the acquisition, exchange, submission and archive of clinical research data and metadata. Its mission is to develop and support global, platform-independent data standards that enable information system interoperability to improve medical research and related areas of healthcare. CDISC standards are vendor-neutral, platform-independent and freely available via the CDISC website.

Proper citation: Clinical Data Interchange Standards Consortium (RRID:SCR_000219) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/chipmeta/

Software using a Hierarchical hidden Markov model for jointly analyzing ChIP-chip and ChIP-seq datasets.

Proper citation: ChIPmeta (RRID:SCR_000054) Copy   

•   Source: SciCrunch Registry

https://www.infoquant.com/oneclickcgh

Platform-independent array copy number analysis software that provides straightforward yet comprehensive detection and reporting of copy number changes.

Proper citation: oneClickCGH (RRID:SCR_000294) Copy   

•   Source: SciCrunch Registry

http://knightadrc.wustl.edu/

The Charles F. and Joanne Knight Alzheimer Disease Research Center (Knight ADRC) supports researchers and our surrounding community in their pursuit of answers that will lead to improved diagnosis and care for persons with Alzheimer disease (AD). The Center is committed to the long-term goal of finding a way to effectively treat and prevent AD. The Knight ADRC facilitates advanced research on the clinical, genetic, neuropathological, neuroanatomical, biomedical, psychosocial, and neuropsychological aspects of Alzheimer disease, as well as other related brain disorders.

Proper citation: Washington University School of Medicine Knight Alzheimers Disease Research Center (RRID:SCR_000210) Copy   

•   Source: SciCrunch Registry

http://www.wavemetrics.com/products/igorpro/igorpro.htm

Software used for visualizing and graphing data, image processing, and programming. It is designed for use by scientists and engineers and supports large data sets, evenly spaced data, and various data import formats. The software includes a suite of image processing operations for image filtering, manipulation, and quantification and is completely programmable.

Proper citation: IGOR Pro (RRID:SCR_000325) Copy   

•   Source: SciCrunch Registry

http://www.dysphonia.org/

The mission of the National Spasmodic Dysphonia Association is to advance medical research into the causes of and treatments for spasmodic dysphonia, promote physician and public awareness of the disorder, and provide support to those affected by spasmodic dysphonia.

Proper citation: National Spasmodic Dysphonia Association (RRID:SCR_000447) Copy   

•   Source: SciCrunch Registry

https://resource.loni.usc.edu/resources/atlases/

Probabilistic reference system for human brain, including tools to establish this reference system for structural and functional anatomy on both macroscopic (in vivo) and microscopic (post mortem) levels. Project has expanded neuroinformatics tools for data sharing and created Conforming Site System that allows laboratories worldwide to contribute data to evolving atlas. Through implementation of ICBM data sharing policy space, they are fostering data exchange while still providing for scientific credit assignment and subject confidentiality.ICBM atlas collection consists of ICBM Template, tool developed to provide reference that includes both set of coordinates and associated anatomical labels; the ICBM 452 T1 atlas, average of T1-weighted MRIs of normal young adult brains, ICBM probabilistic atlases, and Cytoarchitectonic Atlas. ICBM Subject Database is web-based database infrastructure that simplifies image dataset collection, organization and dissemination. Authorized users may view representations of data and form collections of datasets that can be downloaded or fed directly into Pipeline environment for distributed processing and analysis.

Proper citation: International Consortium for Brain Mapping (RRID:SCR_000445) Copy   

•   Source: SciCrunch Registry

http://www.talairach.org/

Software automated coordinate based system to retrieve brain labels from the 1988 Talairach Atlas. Talairach Daemon database contains anatomical names for brain areas using x-y-z coordinates defined by the 1988 Talairach Atlas.

Proper citation: Talairach Daemon (RRID:SCR_000448) Copy   

•   Source: SciCrunch Registry

http://highwire.stanford.edu/

A division of the Stanford University Libraries, which produces the online versions of journals and other scholarly content.

Proper citation: HighWire Press (RRID:SCR_000761) Copy   

•   Source: SciCrunch Registry

http://harvard.eagle-i.net/i/0000012e-58c7-d44f-55da-381e80000000

Core to provide gene expression data analysis service. Activities range from the provision of services to fully collaborative grant funded investigations.

Proper citation: Harvard Partners HealthCare Center for Personalized Genetic Medicine Bioinformatics Core Facility (RRID:SCR_000882) Copy   

•   Source: SciCrunch Registry

http://w3.cns.org/university/webinar/index2.asp

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. A series of of webinars offered directly to users' computers. The webinars are offered in a variety of subjects, including neurotrauma, spine, tumor and vascular. Each webinars costs $35 US and offers CME credit.

Proper citation: University of Neurosurgery Webinar Series (RRID:SCR_000639) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/bait/

Software to create strand inheritance plots in data derived from the Strand-Seq sequencing protocol. The software is designed to be flexible with a range of species, and basic template folders can called to read in species-specific data.

Proper citation: BAIT (RRID:SCR_000511) Copy   

•   Source: SciCrunch Registry

http://www.icpsr.umich.edu/icpsrweb/NAHDAP/

Archive that acquires, preserves and disseminates data relevant to drug addiction and HIV research. Collection of data on drug addiction and HIV infection in United States. Most of datasets are raw data from surveys, interviews, and administrative records. They were originally gathered in research projects and for administrative purposes. Some datasets have been used in published studies. Bibliographies of these studies are available . Provides access to research data and technical assistance for data depositors. Provides e-workshops on data preparation and data systems.

Proper citation: National Addiction and HIV Data Archive Program (NAHDAP) (RRID:SCR_000636) Copy   

•   Source: SciCrunch Registry

http://fulxie.0fees.us/?type=reference&ckattempt=1

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 1,2023. Web-based tool for evaluating and screening reference genes from extensive experimental datasets. It integrates major computational programs (geNorm, Normfinder, BestKeeper, and the comparative delta-Ct method) to compare and rank the tested candidate reference genes. Based on the rankings from each program, it assigns an appropriate weight to an individual gene and calculated the geometric mean of their weights for the overall final ranking., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: RefFinder (RRID:SCR_000472) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/DOID

Comprehensive hierarchical controlled vocabulary for human disease representation.Open source ontology for integration of biomedical data associated with human disease. Disease Ontology database represents comprehensive knowledge base of inherited, developmental and acquired human diseases.

Proper citation: Human Disease Ontology (RRID:SCR_000476) Copy   

•   Source: SciCrunch Registry

http://trace.ddbj.nig.ac.jp/dor/index_e.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Archival database of functional genomics data generated by microarray and highly parallel new generation sequencers. Data are exchanged between ArrayExpress at EBI and DOR in common MAGE-TAB format. Supports MIAME and MINSEQE-compliant data submissions. DOR issues accession numbers, E-DORD-n to experiment and A-DORD-n to array design. DOR exchanges public data with the EBI ArrayExpress in common MAGE-TAB format. Note: At present, DOR does not accept submissions. DDBJ will announce launch of DOR when it is ready. (2013/01/31) The data can be kept private until your paper is published. You can set the hold date for a maximum of 1 year and can change it. Registered records are released according to the Data Release Policy.

Proper citation: DDBJ Omics Archive (RRID:SCR_000597) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/GAZ

THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 23, 2014. Description not available.

Proper citation: Gazetteer (RRID:SCR_000473) Copy   

•   Source: SciCrunch Registry

http://www.du.edu/psychology/

The department of psychology at Denver University that offers degrees at the undergraduate, graduate and doctoral level. The doctoral programs have specializations such as Affect/Social, Child Clinical, Cognitive, and Developmental.

Proper citation: Denver University Department of Psychology (RRID:SCR_000474) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/ATO

A taxonomy of Amphibia

Proper citation: Amphibian Taxonomy Ontology (RRID:SCR_000906) Copy   

•   Source: SciCrunch Registry