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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
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
https://code.google.com/p/dysc/
Software for Greedy Clustering of 16S rRNA Reads which uses a dynamic seeding strategy.
Proper citation: DySC (RRID:SCR_000553) Copy
http://purl.bioontology.org/ontology/SEDI
An ontology for DICOM as used in the SeDI project.
Proper citation: Semantic DICOM Ontology (RRID:SCR_000309) Copy
https://nei.nih.gov/health/clinicalstudies/
An archived portal of clinical studies, both ongoing and completed, that have been conducted and supported by the National Eye Institute (NEI) since 1970. The portal covers corneal diseases, glaucoma, epidemiology, lens and cataract, retinal diseases, strabismus, amblyopia and visual processing.
Proper citation: NEI Clinical Studies (RRID:SCR_000546) Copy
http://www.nitrc.org/projects/scribe/
Scribe encodes papers to populate the BrainMap Database
Proper citation: Scribe (RRID:SCR_000423) 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
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
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
https://sourceforge.net/projects/popbam/
A tool to perform evolutionary or population-based analyses of next-generation sequencing data. POPBAM takes a BAM file as its input and can compute many widely used evolutionary genetics measures in sliding windows across a genome.
Proper citation: POPBAM (RRID:SCR_000464) Copy
http://drfast.sourceforge.net/
A software which maps di-base reads (SOLiD color space reads) to reference genome assemblies in a fast and memory-efficient manner.
Proper citation: drFAST (RRID:SCR_000586) Copy
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
http://genome.crg.es/software/gfftools/GFF2PS.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software program for visualizing annotations of genomic sequences. The program has features such as the ability to create comprehensive plots, customizable parameters, and flexibility in file format.
Proper citation: Genome BioInformatics Research Lab - gff2ps (RRID:SCR_000462) Copy
http://bioinfo2.ugr.es/NGSmethPipe/
A software tool which generates high-quality methylation maps.
Proper citation: NGSmethPipe (RRID:SCR_000583) 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
https://cran.r-project.org/src/contrib/Archive/sybil/
A Systems Biology Library for R, implementing algorithms for constraint based analyses of metabolic networks (e.g. flux-balance analysis (FBA), minimization of metabolic adjustment (MOMA), regulatory on/off minimization (ROOM), robustness analysis and flux variability analysis). This is an implementation of COBRA toolbox in R language.
Proper citation: sybil - Efficient Constrained Based Modelling in R (RRID:SCR_000457) Copy
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
https://github.com/holtjma/msbwt
A software package for creating, merging, and querying multi-string BWTs.
Proper citation: msbwt (RRID:SCR_000458) Copy
http://www.stanford.edu/~cpatton/maxc.html
A series of programs for determining the free metal concentration in the presence of chelators or total metal given a desired free concentration.
Proper citation: MAXCHELATOR (RRID:SCR_000459) 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://bioconductor.org/packages/release/bioc/html/Rdisop.html
Software for identification of metabolites using high precision mass spectrometry. MS Peaks are used to derive a ranked list of sum formulae, alternatively for a given sum formula the theoretical isotope distribution can be calculated to search in MS peak lists.
Proper citation: Rdisop (RRID:SCR_000453) Copy
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