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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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VDJ Server Resource Report Resource Website 10+ mentions |
VDJ Server (RRID:SCR_014356) | web application, data analysis software, data processing software, software application, software resource, collaboration tool | A web application immune repertoire management, analysis, and archiving. Users can collaborate and share data either privately or publicly. Users can perform a variety of tasks, such as create and share projects with other users, conduct pre-processing tasks on single end reads, run IgBlast, and obtain basic repertoire characterization results for B cell receptor and T cell receptor repertoires. | omics data, web application, scalable resource, immune repertoire |
has parent organization: University of Texas Southwestern Medical Center; Texas; USA has parent organization: J. Craig Venter Institute has parent organization: Yale University; Connecticut; USA |
NIAID 1R01A1097403 | Free, Open source analysis software is available for local use | http://wiki.vdjserver.org/vdjserver/index.php/VDJServer_Wiki | SCR_014356 | VDJServer | 2026-08-13 09:29:00 | 18 | |||||||
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Brain Entropy Mapping Toolbox Resource Report Resource Website 10+ mentions |
Brain Entropy Mapping Toolbox (RRID:SCR_014470) | BENtbx | data processing software, software application, software toolkit, software resource, image processing software | A toolkit for mapping brain entropy using fMRI. It uses several functions from ASLtbx. At its core, the toolkit is a collection of batch scripts that implement a pipeline for processing fMRI data in order to get Sample entropy for each voxel. | brain, entropy, fmri, mapping, software toolkit, image processing software | PMID:24657999 | Acknowledgement required, Register to download application and sample data | SCR_014470 | Brain Entropy Mapping Toolbox: BENtbx | 2026-08-13 09:29:02 | 12 | ||||||||
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Rexplore Resource Report Resource Website |
Rexplore (RRID:SCR_014364) | web application, software resource, text-mining software, software application | An application which provides an environment to explore and organize scholarly data. Rexplore leverages solutions in large-scale data mining, semantic technologies and visual analytics, which allows users to detect and follow research trends, identify and map relationships between authors, perform expert searches, and analyze research performance. | semantic publishing, analytics, semantic web, machine learning, data mining | has parent organization: Open University; Milton Keynes; United Kingdom | Not publicly available, Contact Enrico Motta | SCR_014364 | 2026-08-13 09:29:02 | 0 | ||||||||||
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CopyCaller Resource Report Resource Website 100+ mentions |
CopyCaller (RRID:SCR_014486) | data analysis software, data processing software, software resource, software application | 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. | data analysis, real-time pcr data analysis, real-time pcr, pcr, dna target | SCR_014486 | 2026-08-13 09:29:03 | 344 | ||||||||||||
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Minitab Resource Report Resource Website 5000+ mentions |
Minitab (RRID:SCR_014483) | data analysis software, data processing software, software resource, software application | 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. | data analysis, statistical analysis, hypothesis, confidence, descriptive | is listed by: SoftCite | SCR_014483 | 2026-08-13 09:29:03 | 6109 | |||||||||||
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Optseq Resource Report Resource Website 100+ mentions |
Optseq (RRID:SCR_014363) | data processing software, software application, standalone software, data acquisition software, software resource | Software tool for automatically scheduling events for rapid-presentation event-related (RPER) fMRI experiments (the schedule is the order and timing of events). Events in RPER are presented closely enough in time that their hemodynamic responses will overlap. This requires that the onset times of the events be jittered in order to remove the overlap from the estimate of the hemodynamic response. RPER is highly resistant to habituation, expectation, and set because the subject does not know when the next stimulus will appear or which stimulus type it will be. | fmri, scheduling event, event, rper, hemodynamic response, stimulus, stochastic design | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Available for download | SCR_005976, nlx_151349 | http://www.nitrc.org/projects/optseq | SCR_014363 | Optseq2, Optseq - fMRI Event Scheduler | 2026-08-13 09:29:00 | 341 | |||||||
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BD CellQuest Pro Resource Report Resource Website 1000+ mentions |
BD CellQuest Pro (RRID:SCR_014489) | data acquisition software, data processing software, software resource, software application | 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. | data analysis, flow cytometry data acquisition and analysis | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014489 | 2026-08-13 09:29:03 | 3939 | |||||||||||
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BayesTraits Resource Report Resource Website 100+ mentions |
BayesTraits (RRID:SCR_014487) | data analysis software, data processing software, software resource, software application | 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. | data analysis software, evolution, phylogeny, evolutionary model | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014487 | 2026-08-13 09:29:11 | 308 | |||||||||||
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Clone Manager Software Resource Report Resource Website 10+ mentions |
Clone Manager Software (RRID:SCR_014521) | data processing software, simulation software, software application, workflow software, software resource | 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. | workflow software, simulation software, enzyme, clone, cloning simulation, graphic map, sequence, view, edit | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014521 | 2026-08-13 09:29:12 | 49 | |||||||||||
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Free Pascal Compiler Resource Report Resource Website 10+ mentions |
Free Pascal Compiler (RRID:SCR_014360) | FPC, FPK | software development environment, software resource, software development tool, software application | Free Pascal is a 32, 64 and 16 bit professional Object Pascal compiler targeting multiple processor architectures and operating systems. Documentation, including guides and manuals, are available on the website. | software development environment, software development tool, compiler, pascal, object pascal |
is used by: CyberUnits is used by: SimulAdren is related to: Lazarus IDE |
Free for download as source code, Pre-compiled for multiple platforms | SCR_014360 | 2026-08-13 09:29:02 | 21 | |||||||||
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Clickjoint Resource Report Resource Website 1+ mentions |
Clickjoint (RRID:SCR_014482) | data analysis software, data processing software, software resource, software application | 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. | image analysis, tracking algorithm, animal movement, animal joint | SCR_014482 | 2026-08-13 09:29:02 | 3 | ||||||||||||
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NIS-Elements Resource Report Resource Website 1000+ mentions Rating or validation data |
NIS-Elements (RRID:SCR_014329) | data analysis software, data processing software, software application, software toolkit, software resource | Microscope imaging software suite used with Nikon products. NIS-Elements includes software applications for advanced and standard research, documentation, confocal microscopy, and high-content analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | element, microscope imaging software, software suite, nikon |
is listed by: SoftCite works with: Nikon: ECLIPSE Ti2 inverted microscope |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014329 | Nikon Instruments Software Elements, NIS Elements, Nikon Instruments Software | 2026-08-13 09:29:00 | 3515 | |||||||||
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IMAGIC Resource Report Resource Website 100+ mentions |
IMAGIC (RRID:SCR_014447) | data processing software, software application, image analysis software, software resource, image processing software | An image analysis software that can process spectra and other multi-dimensional data-sets. The software package is aimed at processing large data sets from (cryo-) electron microscopy, especially in the field of single particle analyses. This software can be used with light and raster-tunneling microscopes, computer tomographs, FT-IR spectrometers and other signal collecting devices. This resource provides three-dimensional data processing and angular reconstitution modules that allow the three-dimensional reconstruction with point-group symmetry from the two dimensional electron microscopy projections. These models aid in the analysis of the macromolecules. | image analysis, spectra, multi-dimensional data, macromolecule, 3d processing, tomograph, spectrometer, software environment | is listed by: SoftCite | PMID:8742718 | Commercial, Account needed for download | SCR_014447 | 2026-08-13 09:29:02 | 217 | |||||||||
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AMT Image Capture Software Resource Report Resource Website 1+ mentions |
AMT Image Capture Software (RRID:SCR_014333) | data processing software, software application, image analysis software, image acquisition software, data acquisition software, software resource, image processing software | AMT camera system software that performs digital image acquisition, processing, and storage. An operations manual and software specifications are available on the main site. | camera operating software, system management software, digital image acquisition, digital image processing, digital image storage | Only for AMT camera systems | SCR_014333 | 2026-08-13 09:29:02 | 5 | |||||||||||
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Macrogen Resource Report Resource Website 5000+ mentions |
Macrogen (RRID:SCR_014454) | biomaterial analysis service, material analysis service, analysis service resource, production service resource, service resource | A company that provides a variety of next generation sequencing services. The company provides researchers with whole genome resequencing, exome sequencing, targeted sequencing, transcriptomics, and epigenome sequencing. | sequencing assay, sequencing analysis software, next generation sequencing | is affiliated with: Axeq Technologies | Commercial entity | SCR_014454 | Macrogen Inc. | 2026-08-13 09:29:02 | 6322 | |||||||||
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SCRATCH Resource Report Resource Website 100+ mentions |
SCRATCH (RRID:SCR_014291) | data access protocol, analysis service resource, production service resource, service resource, web service, software resource | Web protein structure and structural feature prediction server.Software suite includes predictors for secondary structure, relative solvent accessibility, disordered regions, domains, disulfide bridges, single mutation stability, residue contacts versus average, individual residue contacts and tertiary structure. User provides amino acid sequence and selects desired predictions, then submits to the server. | Protein predictor, secondary structure, relative solvent accessibility, disordered regions, domains, disulfide bridges, single mutation stability, residue contacts versus average, individual residue contacts, tertiary structure prediction, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:15980571 | Free, Freely available | biotools:scratch | https://bio.tools/scratch | http://www.igb.uci.edu/servers/psss.html | SCR_014291 | Scratch Protein Predictor | 2026-08-13 09:29:09 | 141 | |||||
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Biobserve Viewer Resource Report Resource Website 10+ mentions |
Biobserve Viewer (RRID:SCR_014337) | data analysis software, data processing software, software application, data acquisition software, software resource | Software that provides subject tracking with body axis alignment and angle of view, which is then used to track body, nose and tail movements without marking the animal. Users may create the scoring system used by the software, as well as zones to observe, quantify, and compare the behavior of an animal in one or more areas. The software features several data acquisition and analysis tools to gather and interpret the data. | mouse, animal tracking, behavior, data acquisition software, data analysis software | Pay for product | SCR_014337 | Bio Observe Viewer | 2026-08-13 09:29:02 | 12 | ||||||||||
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Andor iQ Resource Report Resource Website 100+ mentions |
Andor iQ (RRID:SCR_014461) | data processing software, software application, image analysis software, software resource, image processing software | A live cell imaging software that allows for control of iXon EMCCD and sCMOS cameras in synchronized combination with a number of additional imaging hardware devices. iQ can be used to run experiments to investigate dynamic processes in both single cells and multicellular systems, image fixed samples, and generate 3 dimensional image volumes for analysis. | image acquisition and analysis, iXon, sCMOS, EMCCD, live cell, 3d image | Public | SCR_014461 | 2026-08-13 09:29:11 | 255 | |||||||||||
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ClinProTools Resource Report Resource Website 100+ mentions |
ClinProTools (RRID:SCR_014341) | data analysis software, data processing software, software application, data acquisition software, software resource | Biomarker detection and evaluation software which provides an advanced basis for mining unknown potential biomarkers in complex protein profiles. Visualization tools such as stack plots and box-and-whiskers plots can be used to interactively inspect and compare large data sets originating from samples that contain different clinical diagnoses. ClinProTools also supplies sophisticated mathematical algorithms for the discovery of complex biomarker pattern models. Besides validation, class-prediction tools are also integrated to allow the implementation of the whole biomarker detection and evaluation process. | biomarker detection, biomarker evaluation, mining, visualization tools, large data set, biomarker pattern model | Pay for product | SCR_014341 | 2026-08-13 09:29:00 | 274 | |||||||||||
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ScanImage Resource Report Resource Website 500+ mentions |
ScanImage (RRID:SCR_014307) | data processing software, software application, signal processing software, data acquisition software, software resource | Open source software application for laser scanning microscopy, electrophysiology, laser scanning photostimulation, and other physiological methods focused on neurobiology. Used to control laser scanning microscopes without need for custom data acquisition hardware. Standard data acquisition boards are used to acquire data and control laser scanning. The tasks of signal integration and image processing are placed on the computer CPU. Multiple versions of ScanImage are available, each with their own features. | Laser, scanning, microscopy, electrophysiology, photostimulation, neurobiology, control, data, acquisition, BRAIN Initiative |
is recommended by: BRAIN Initiative has parent organization: Cold Spring Harbor Laboratory has parent organization: Northwestern University; Illinois; USA |
PMID:12801419 | Restricted | http://scanimage.vidriotechnologies.com/display/SIH/ScanImage+Home | SCR_014307 | Scan Image, ScanImage | 2026-08-13 09:28:59 | 876 |
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