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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.
http://www.imagemagick.org/script/index.php
Software suite for creating, editing, composing, and converting bitmap images. It can read and write images in over 200 formats including PNG, JPEG, JPEG-2000, GIF, TIFF, DPX, EXR, WebP, Postscript, PDF, and SVG. The user can use this software to resize, flip, mirror, rotate, distort, shear and transform images, adjust image colors, apply various special effects, or draw text, lines, polygons, ellipses and Bézier curves.
Proper citation: ImageMagick (RRID:SCR_014491) Copy
A program that searches PubMed to generate a heat map using a user's search terms. It also allows you to see over the years how many publications there are with the user's search term(s).
Proper citation: pubatlas.org (RRID:SCR_014538) Copy
Commercial software tool designed to function as a multiplatform instrument controlling environment for NIRx products. Its features include the ability to run full or partial sensing configurations, montage views and viewing options, and a real-time system status reporting display.
Proper citation: NIRStar (RRID:SCR_014540) Copy
A forum for preclinical data sharing and interpretation to enhance its utility for clinical research and development. The forum allows researchers to communicate and collaborate on modern preclinical issues and data sharing.
Proper citation: Preclinical Data Forum Network (RRID:SCR_014545) Copy
http://www.celllineauthentication.com/
A material analysis service of the commercial organization Genetica DNA Laboratories which provides authentication of human cancer cell lines, stem cell lines and xenografts utilizing STR DNA technology.
Proper citation: Cell Line Authentication Testing (RRID:SCR_014504) Copy
A persistent unique identifier for samples and specimens collected from the natural environment. IGSNs are created by the user and are case sensitive. They should be concise, machine readable, and non-derivable to ensure originality. IGSNs were created and are organized by the IGSN e.V., whose goal is to implement and promote standard methods for locating, identifying, and citing physical samples with confidence by operating an international IGSN registration service with a distributed infrastructure for use by and benefit to its members.
Proper citation: International Geo Sample Number (RRID:SCR_014505) Copy
http://zhanglab.ccmb.med.umich.edu/I-TASSER/
Web server as integrated platform for automated protein structure and function prediction. Used for protein 3D structure prediction. Resource for automated protein structure prediction and structure-based function annotation.
Proper citation: I-TASSER (RRID:SCR_014627) Copy
http://www.vsni.co.uk/products/genstat/
A statistical software which can be used for basic statistics, experimental design, sample size calculations, and analysis of linear mixed models, time series, and spatial analysis.
Proper citation: GenStat (RRID:SCR_014595) Copy
A software used to control and operate the Applied Biosystems 7500 Real-Time PCR system.
Proper citation: 7500 Real-Time PCR Software (RRID:SCR_014596) Copy
http://chemistry.unt.edu/~verbeck/LIMS/Manuals/XCAL_Quant.pdf
A software which acquires and processes data sets, primarily through the Xcalibur system.
Proper citation: Thermo Xcalibur (RRID:SCR_014593) Copy
http://cole-trapnell-lab.github.io/cufflinks/cuffmerge/
Software tool for transcriptome assembly and differential expression analysis for RNA-Seq. Includes script called cuffmerge that can be used to merge together several Cufflinks assemblies. It also handles running Cuffcompare as well as automatically filtering a number of transfrags that are likely to be artifacts. If the researcher has a reference GTF file, the researcher can provide it to the script to more effectively merge novel isoforms and maximize overall assembly quality.
Proper citation: Cufflinks (RRID:SCR_014597) Copy
http://cyberinncorp.com/SigmaGel.htm
Gel analysis software which can be used on a PC with TWAIN-compatible scanners without specialty equipment. Users scan or load an image which can then be calibrated. SigmaGel allows users to make lane measurements, spot measurements, and molecular weight measurements. After data analysis was completed, users can print or copy and paste data and images.
Proper citation: SigmaGel Software (RRID:SCR_014598) Copy
http://www.cbn-atl.org/research/stopwatch.shtml
A software which tracks the number of occurrences and duration of up to 16 defined events. The user can group events together so that turning on one event in a group will automatically turn off other active events in the group. Sessions can end after a fixed length of time, or the sessions can be ended manually, At the end of the session, the data can be saved in a comma-delimited file which can be easily imported into a spreadsheet application.
Proper citation: Stopwatch+ (RRID:SCR_014591) Copy
http://statplus-mac.en.softonic.com/mac
A statistical data analysis tool that works with Microsoft Excel and is designed especially for use in IOS systems. Tutorials and examples are provided within the program.
Proper citation: StatPlus Mac (RRID:SCR_014635) Copy
http://www6.appliedbiosystems.com/support/software/copycaller/CopyCallerUserGuide.pdf
A software for analyzing real-time PCR data and quantifying DNA targets. It can perform copy number analysis, report confidence in copy number, display data in table and graphic format, change analysis parameters, and view data analysis information for multiple experiments at once.
Proper citation: CopyCaller (RRID:SCR_014486) Copy
https://www.minitab.com/en-us/products/minitab/
A statistical software package that allows the user to import data, create graphs, and perform statistical analysis. It can perform basic statistical tests like descriptive statistics, hypothesis tests, confidence intervals, and normality tests as well as regression and ANOVA and quality assessment.
Proper citation: Minitab (RRID:SCR_014483) Copy
https://www.bdbiosciences.com/documents/15_cellquest_prosoft_analysis.pdf
A software for acquiring and analyzing flow cytometry data. The user can create plots with elements like regions, gates, statistics, markers, and annotated text. The software can also be used for batch analysis or quality control of analysis. Results can be exported and saved., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: BD CellQuest Pro (RRID:SCR_014489) Copy
http://www.evolution.rdg.ac.uk/BayesTraits.html
A computer package for performing analyses of trait evolution among groups of species for which a phylogeny or sample of phylogenies is available. It incorporates earlier programs including Multistate, Discrete and Continuous. BayesTraits can be applied to the analysis of traits that adopt a discrete number of states, or to the analysis of continuously varying traits. Hypotheses can be tested about models of evolution, ancestral states and correlations among pairs of traits., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: BayesTraits (RRID:SCR_014487) Copy
http://www.scied.com/pr_cmbas.htm
A software system to assist with cloning simulation, enzyme operations, and graphic map drawing. Clone Manager can also be used as a way to view or edit sequence files, find open reading frames, translate genes, or find genes or text in files. Clone Manager Professional is an upgraded version of Clone Manager Basic., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Clone Manager Software (RRID:SCR_014521) Copy
http://aleasol.ch/cms/index.php/clickjoint.en.html
A software for analyzing animal movement on videos and images. The user can define the animal's joints so the software can analyze using a tracking algorithm.
Proper citation: Clickjoint (RRID:SCR_014482) Copy
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