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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://medicine.utah.edu/

An university in Utah which provides opportunities in teaching, research and clinical experience for developing physicians. This organization provides MD degrees, physician training, residency, fellowship specialty training and degrees in public health or research.

Proper citation: University of Utah School of Medicine; Utah; USA (RRID:SCR_000339) 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://sourceforge.net/projects/fqzcomp/

A basic fastq compressor, designed primarily for high performance.

Proper citation: fqzcomp (RRID:SCR_000299) Copy   

•   Source: SciCrunch Registry

http://www.darpa.mil/

A military affiliated research institute which focuses on funding and approving new and ongoing programs while ensuring a balanced investment portfolio. This organization is mainly concerned with making investments in technologies that can be used for national security.

Proper citation: Defense Advanced Research Projects Agency (RRID:SCR_000330) Copy   

•   Source: SciCrunch Registry

http://www.indeed.com/

A database of job listings

Proper citation: Indeed (RRID:SCR_000292) 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.genebridges.com/

A biotech company that commercializes its patented Red/ET recombination worldwide as licenses and supplies several products for the pharmaceutical and biotech industry as well as academia. It operates from the Technologie Park in Heidelberg and provides customized in-house DNA modification of any kind. Recombineering with Red/ET allows cloning, subcloning and modification of DNA at any chosen position. It permits precise engineering of DNA molecules of any size, including very large ones such as BACs or the E.coli chromosome.

Proper citation: Gene Bridges (RRID:SCR_000483) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/mirprimer/

Software tool for automatic design of primers for PCR amplification of microRNAs using the method miR-specific RT-qPCR (Balcells, I., Cirera, S., and Busk, P.K. (2011). Specific and sensitive quantitative RT-PCR of miRNAs with DNA primers. BMC Biotechnol. 11, 70).

Proper citation: miRprimer (RRID:SCR_000480) 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.arb-home.de/

Software environment for maintaining databases of molecular sequences and additional information, and for analyzing the sequence data, with emphasis on phylogeny reconstruction. Programs have primarily been developed for ribosomal ribonucleic acid (rRNA) sequences and, therefore, contain special tools for alignment and analysis of these structures. However, other molecular sequence data can also be handled. Protein gene sequences and predicted protein primary structures as well as protein secondary structures can be stored in the same database. ARB package is designed for graphical user interface. Program control and data display are available in a hierarchical set of windows and subwindows. Majority of operations can be controlled using mouse for moving pointer and the left mouse button for initiating and performing operations.

Proper citation: ARB project (RRID:SCR_000515) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/pyqpcr/

A GUI application written in python that deals with quantitative PCR (QPCR) raw data. Using quantification cycle values extracted from QPCR instruments, it uses a proven and universally applicable model to give finalized quantification resu

Proper citation: pyQPCR (RRID:SCR_000471) 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://cbrain.mcgill.ca/loris

A modular and extensible web-based data management system that integrates all aspects of a multi-center study, from heterogeneous data acquisition to storage, processing and ultimately dissemination, within a streamlined platform. Through a standard web browser, users are able to perform a wide variety of tasks, such as data entry, 3D image visualization and data querying. LORIS also stores data independently from any image processing pipeline, such that data can be processed by external image analysis software tools. LORIS provides a secure web-based and database-driven infrastructure to automate the flow of clinical data for complex multi-site neuroimaging trials and studies providing researchers with the ability to easily store, link, and access significant quantities of both scalar (clinical, psychological, genomic) and multi-dimensional (imaging) data. LORIS can collect behavioral, neurological, and imaging data, including anatomical and functional 3D/4D MRI models, atlases and maps. LORIS also functions as a project monitoring and auditing platform to oversee data acquisition across multiple study sites. Confidentiality during multi-site data sharing is provided by the Subject Profile Management System, which can perform automatic removal of confidential personal information and multiple real-time quality control checks. Additionally, web interactions with the LORIS portal take place over an encrypted channel via SSL, ensuring data security. Additional features such as Double Data Entry and Statistics and Data Query GUI are included.

Proper citation: LORIS - Longitudinal Online Research and Imaging System (RRID:SCR_000590) Copy   

•   Source: SciCrunch Registry

https://github.com/feizhe/PGS

Software tool for association study of high-dimensional microRNA expression data with repeated measures. The penalized regression model incorporates a grid search method for analyzing associations of high-dimensional microRNA expression data with repeated measures.

Proper citation: PGS (RRID:SCR_000475) 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://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://www.ecnp.eu/

A pan-European scientific association to encourage research across the neurosciences and to translate new knowledge on fundamental disease mechanisms into new medicines and clinical applications. As an interdisciplinary forum for the science and treatment of disorders of the brain, they promote the communication and cross- fertilization of high-quality experimental and clinical research across the field of neuroscience. ECNP is a non-profit member-based association, independently governed and self-funded. ECNP is a public-interest-serving entity.

Proper citation: ECNP (RRID:SCR_000501) Copy   

•   Source: SciCrunch Registry

https://github.com/cc2qe/speedseq

Software for a lightweight, flexible, and open source pipeline that identifies genomic variation (single nucleotide variants (SNVs), indels, and structural variants (SVs)).

Proper citation: SpeedSeq (RRID:SCR_000469) Copy   

•   Source: SciCrunch Registry