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http://www.allegheny.edu/

A private liberal arts college that offers degrees in social sciences, humanities and natural sciences at the undergraduate level.

Proper citation: Allegheny College; Pennsylvania; USA (RRID:SCR_000369) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/site/beckerjeremie/home/nucleofinder

A software for a statistical approach for the detection of nucleosome positions in a cell population. The software identifies important features of nucleosome organization such as the spacing downstream of active promoters and the enrichment and depletion of GC/AT dinucleotides of in vitro nucleosomes.

Proper citation: NucleoFinder (RRID:SCR_000368) Copy   

•   Source: SciCrunch Registry

https://github.com/yongchao/flowPeaks

Software for fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means.

Proper citation: flowPeaks (RRID:SCR_000407) Copy   

•   Source: SciCrunch Registry

https://github.com/mickaelleclercq/mirdup

A software used for the validation of pre-miRNAs predictions as well as predict the final structure of mature miRNA.

Proper citation: MiRdup (RRID:SCR_000316) Copy   

•   Source: SciCrunch Registry

https://posit.co/

Open source and enterprise ready professional software for R statistical computing environment. Integrated development environment for R. Includes console, syntax highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management. Available in open source and commercial editions and runs on desktop Windows, Mac, and Linux or in browser connected to RStudio Server or RStudio Server Pro (Debian/Ubuntu, RedHat/CentOS, and SUSE Linux).

Proper citation: RStudio (RRID:SCR_000432) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/QUALIFIER.html

Software that provides quality control and quality assessment tools for gated flow cytometry data.

Proper citation: QUALIFIER (RRID:SCR_000389) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/scribe/

Scribe encodes papers to populate the BrainMap Database

Proper citation: Scribe (RRID:SCR_000423) Copy   

•   Source: SciCrunch Registry

http://graphpad.com/

A commercial graphing software company that offers scientific software for statistical analyses, curve fitting and data analysis. It offers four programs: Prism, InStat, StatMate and QuickCalcs.

Proper citation: GraphPad (RRID:SCR_000306) Copy   

•   Source: SciCrunch Registry

http://www.altmetric.com/bookmarklet.php

Free bookmarklet for Chrome, Firefox and Safari that allows you to instantly get article level metrics for any recent paper. Simply drag the button below to your bookmarks bar, navigate to a journal article page, and hit Altmetric it!

Proper citation: Altmetric Bookmarklet (RRID:SCR_000427) Copy   

•   Source: SciCrunch Registry

http://wustl.edu/

Private research university in Greater St. Louis with its main campus mostly in unincorporated St. Louis County, Missouri and Clayton, Missouri.

Proper citation: Washington University in St. Louis; Missouri; USA (RRID:SCR_000343) Copy   

•   Source: SciCrunch Registry

http://wzar.unizar.es/servicios/ingles/prese.htm

An undergraduate and postgraduate university which is located in Zaragoza, Spain.

Proper citation: University of Zaragoza; Zaragoza; Spain (RRID:SCR_000341) Copy   

•   Source: SciCrunch Registry

https://www.uzh.ch/en.html

University located in Zürich, Switzerland was founded in 1833. Has faculties in Philosophy, Human Medicine, Economic Sciences, Law, Mathematics and Natural Sciences, Theology and Veterinary Medicine. Offers the widest range of subjects and courses of any Swiss higher education institution. As of October 2018, 23 Nobel laureates and 1 Turing Award winner have been affiliated with University of Zurich as alumni, faculty or researchers.

Proper citation: University of Zurich; Zurich; Switzerland (RRID:SCR_000342) 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

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.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://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