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A software for genome assembly, and is specifically designed to analyze long Sanger-chemistry reads.
Proper citation: ARACHNE (RRID:SCR_000351) Copy
http://parsecnv.sourceforge.net/
Software that takes CNV calls as input and creates SNP based statistics for CNV occurrence in cases and controls then calls CNVRs based on neighboring SNPs of similar significance.
Proper citation: ParseCNV (RRID:SCR_000355) Copy
http://sourceforge.net/projects/kinannote/
Software that identifies and classifies protein kinases in a user-provided fasta file using an HMM derived from serine / threonine protein kinases, a position specific scoring matrix derived from the HMM, and comparison with a local version of the curated kinase database from kinase.com.
Proper citation: Kinannote (RRID:SCR_000352) Copy
A genome browser framework which gives an open browsing experience, open data access, collaborative work support, and a framework to import annotations. Multiple data access approaches are supported for external platforms to retrieve data from ABrowse. This resource also contains an online user-space in which users can create, store and share comments, annotations and landmarks.
Proper citation: ABrowse (RRID:SCR_000345) Copy
International consortium of six centers assembled to participate in the development and implementation of studies to identify infectious agents, dietary factors, or other environmental agents, including psychosocial factors, that trigger type 1 diabetes in genetically susceptible people. The coordinating centers recruit and enroll subjects, obtaining informed consent from parents prior to or shortly after birth, genetic and other types of samples from neonates and parents, and prospectively following selected neonates throughout childhood or until development of islet autoimmunity or T1DM. The study tracks child diet, illnesses, allergies and other life experiences. A blood sample is taken from children every 3 months for 4 years. After 4 years, children will be seen every 6 months until the age of 15 years. Children are tested for 3 different autoantibodies. The study will compare the life experiences and blood and stool tests of the children who get autoantibodies and diabetes with some of those children who do not get autoantibodies or diabetes. In this way the study hopes to find the triggers of T1DM in children with higher risk genes.
Proper citation: TEDDY (RRID:SCR_000383) Copy
http://www.massachusetts.edu/index.html
A five-campus public university system in Massachusetts. The system includes four universities, a medical school, and a satellite campus.
Proper citation: University of Massachusetts; Massachusetts; USA (RRID:SCR_000379) Copy
http://www.nitrc.org/projects/mri_lbptop/
The packaged tools perform Local Binary Pattern on Three Orthogonal Planes (LBP-TOP) analysis on MR brain images. One can use them to extract LBP texture features for machine learning applications or other advance analysis. Bash scripts performing simple preprocessing with FSL and AFNI as well as LBP mapping programs written by Java are both including in this package. The output is the histogram describing the brain morphology.
Proper citation: Local Binary Pattern Analysis Tools for MR Brain Images (RRID:SCR_000412) Copy
Software package for control of automated microscopes. Cross-platform desktop application, to control motorized microscopes, scientific cameras, stages, illuminators, and other microscope accessories.
Proper citation: uManager (RRID:SCR_000415) Copy
A supplier of various biochemical products for research in pharmacy and biotechnology as well as the specialty ingredients market. Examples of products include active pharmaceutical ingredients, stem cell therapies, drinking water sanitizers and agriculture services and products.
Proper citation: Lonza (RRID:SCR_000377) Copy
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
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
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
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
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
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
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
http://sourceforge.net/projects/fqzcomp/
A basic fastq compressor, designed primarily for high performance.
Proper citation: fqzcomp (RRID:SCR_000299) Copy
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
A database of job listings
Proper citation: Indeed (RRID:SCR_000292) Copy
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
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