Searching across hundreds of databases
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
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.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Phyutility Resource Report Resource Website 10+ mentions |
Phyutility (RRID:SCR_018545) | data analysis software, data processing software, software application, software resource | Command line program that performs analyses or modifications on both trees and data matrices. Software phyloinformatics tool for trees, alignments and molecular data. Used for summarizing and manipulating phylogenetic trees, manipulating molecular data and retrieving data from NCBI. | Data matrice analysis, data matrice modification, phyloinformatics, phylogenetic tree, alignment, molecular data manipulation, data analysis |
is listed by: Debian is listed by: OMICtools is listed by: SoftCite is related to: NCBI |
NSF Cyberinfrastructure for Phylogenetic Research EF 0331654 | PMID:18227120 | Free, Freely available | OMICS_21687 | https://sources.debian.org/src/phyutility/ | SCR_018545 | 2025-05-12 11:20:01 | 40 | ||||||
|
CuGenDB Resource Report Resource Website 100+ mentions |
CuGenDB (RRID:SCR_018401) | CuGenDB | topical portal, portal, data or information resource, database | Database to facilitate genomic and genetic data distribution, analysis, mining and integration for cucurbits. To store, mine, analyze, integrate and disseminate Cucurbitaceae family datasets and to provide central portal for cucurbit research and breeding community. Central portal for comparative and functional genomics of cucurbit crops. | Genomic data, genetic data, cucurbit, data distribution, data analysis, data mining, data integration, dataset, comparative genomics, functional genomics, cucurbit crop, FASEB list | USDA National Institute of Food and Agriculture Specialty Crop Research Initiative ; US-Israel Binational Agricultural Research and Development Fund ; USDA Agricultural Research Service ; International Cucurbit Genomics Initiative |
PMID:30321383 | Free, Freely available | SCR_018401 | Cucurbit Genomics Database, Cucurbitaceae family Genomics Database | 2025-05-12 11:19:54 | 150 | |||||||
|
Imspector Resource Report Resource Website 50+ mentions |
Imspector (RRID:SCR_018863) | data analysis software, data processing software, software application, software resource | Software tool for real time analysis and data visualization. Software system for experimental control and quantitative data analysis in microscopy and spectroscopy.Integration of data processing and acquisition allows real time analysis and visualization of experimental results. | Data analysis, real time data, visualization, quantitative analysis, microscopy, spectroscopy | Free, Freely available | https://github.com/AbberiorInstruments/ImspectorDocs/blob/master/docs/intro.rst https://imspector.abberior-instruments.com/ |
SCR_018863 | 2025-05-12 11:20:20 | 70 | ||||||||||
|
Muscle X Resource Report Resource Website 1+ mentions |
Muscle X (RRID:SCR_018811) | data processing software, image analysis software, software application, software toolkit, software resource, data analysis software | Software suite as collection of programs intended to assist with analyzing diffraction X-ray images. MuscleX diffraction X-ray image analyzing toolkit. Data reduction software for X-ray fiber diffraction data. | Diffraction analysis, x ray image, diffraction X-Ray image analysis, X-ray data, X-ray fiber diffraction data, data analysis, data reduction | has parent organization: Illinois Institute of Technology; Illinois; USA | Free, Available for download, Freely available | https://sourceforge.net/projects/musclex/files/ | SCR_018811 | MuscleX, Muscle X 1.14.12 | 2025-05-12 11:20:18 | 3 | ||||||||
|
UCSC Xena Resource Report Resource Website 1000+ mentions |
UCSC Xena (RRID:SCR_018938) | web service, software resource, portal, data or information resource, data access protocol, analysis service resource, production service resource, service resource | Web tool where one component is front end Xena Browser and another component is back end Xena Hubs. Web based Xena Browser empowers biologists to explore data across multiple Xena Hubs with variety of visualizations and analyses. Xena Hubs host genomics data from laptops, public servers, behind firewall, or in cloud, and can be public or private. Xena Browser receives data simultaneously from multiple Xena Hubs and integrates them into single coherent visualization within browser. Allows users to explore functional genomic data sets for correlations between genomic and/or phenotypic variables. | Data visualization, data analysis, genomics data, explore functional genomic data, functional genomic, data sets, genomic variable correlation, phenotypic variables correlation | has parent organization: University of California at Santa Cruz; California; USA | Free, Freely available | https://xenabrowser.net/ | SCR_018938 | UCSC Xena Browser, Xena Browser | 2025-05-12 11:20:27 | 2097 | ||||||||
|
o²S²PARC Resource Report Resource Website 1+ mentions |
o²S²PARC (RRID:SCR_018997) | osparc | software resource, software application, simulation software | Simulation platform that enables users to create, access, tune, and run models or computational algorithms through web based interface. Web interactive simulation platform that hosts SPARC computational models and solvers. Allows collaborative development and sharing, model coupling and cloud based execution, data visualization and analysis, and ensures sustainability of computational models developed within SPARC. Enables users to create predictive, multiscale, multi-physics models spanning from modulation sources acting on peripheral nervous system (PNS) to resulting modulation of organ functional response. | SPARC, SPARC computational model, data sharing, model coupling, cloud based execution, data visualization, data analysis, peripheral nervous system, organ functional response |
is used by: SPARC Project is organization facet of: SPARC Project |
Free, Freely available | SCR_018997 | open online Simulation platform for Stimulating Peripheral Activity to Relieve Conditions | 2025-05-12 11:20:33 | 1 | ||||||||
|
NanoGalaxy Resource Report Resource Website 1+ mentions |
NanoGalaxy (RRID:SCR_018912) | data processing software, web service, data visualization software, software application, software resource, software toolkit, data analysis software, data access protocol | Webserver to process, analyse and visualize Oxford Nanopore Technologies (ONT) data and similar long-reads technologies. Collection of best practice and popular ONT-oriented tools are integrated in this custom Galaxy instance. | European Galaxy Project, Oxford Nanopore Technologies, Oxford Nanopore Technologies data, data analysis, long reads technology, ONT oriented tools collection, custom Galaxy instance, , Galaxy, Nanopore, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Galaxy is related to: University of Freiburg; Baden-Wurttemberg; Germany |
Free, Freely available | biotools:nanogalaxy | https://galaxyproject.org/use/nanogalaxy/ https://bio.tools/nanogalaxy |
SCR_018912 | 2025-05-12 11:20:24 | 6 | ||||||||
|
Progenesis QI Resource Report Resource Website 500+ mentions |
Progenesis QI (RRID:SCR_018923) | data analysis software, data processing software, software application, software resource | Software tool as next generation in LC-MS proteomics data analysis software by Nonlinear Dynamics. | Next generation, LC-MS proteomics data, data analysis, Nonlinear Dynamics | Free, Available for download, Freely available | SCR_018923 | 2025-05-12 11:20:25 | 599 | |||||||||||
|
TRiCoLOR Resource Report Resource Website 1+ mentions |
TRiCoLOR (RRID:SCR_018801) | data processing software, software application, software resource, sequence analysis software, data analysis software | Command line application for tandem repeats profiling from error prone long read sequencing data. Works on data from Oxford Nanopore Technologies and Pacific Biosciences sequencers. Used on whole genome alignments. | Tandem repeat, long read sequencing data, whole genome alignment, data analysis, sequence analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:tricolor | https://bio.tools/tricolor | SCR_018801 | 2025-05-12 11:20:17 | 2 | ||||||||
|
Toolbox for Representational Similarity Analysis Resource Report Resource Website 1+ mentions |
Toolbox for Representational Similarity Analysis (RRID:SCR_019029) | data processing software, software application, software toolkit, software resource, data analysis software | Software Matlab toolbox to perform representational similarity analysis for neural data. | Representional similarity analysis, data analysis, data, neural data |
is related to: MATLAB has parent organization: University of Cambridge; Cambridge; United Kingdom |
UK Medical Research Council ; European Research Council Starting Grant ; European Research Council Advanced Grant |
PMID:24743308 | Free, Available for download, Freely available | SCR_019029 | RSA toolbox | 2025-05-12 11:20:34 | 5 | |||||||
|
IDseq Resource Report Resource Website 10+ mentions |
IDseq (RRID:SCR_019038) | topical portal, portal, organism-related portal, data or information resource, analysis service resource, production service resource, service resource | Open source cloud based pipeline and analysis service for metagenomic pathogen detection and monitoring. Hypothesis free global software platform that helps scientists identify pathogens in metagenomic sequencing data. IDseq Portal accepts raw mNGS data, performs host and quality filtration steps, then executes assembly based alignment pipeline which results in assignment of reads and contigs to taxonomic categories. | Metagenomic pathogen detection, metagenomic pathogen monitoring, identify pathogens, metagenomic sequencing data, data analysis | Chan Zuckerberg Initiative | DOI:10.1101/2020.04.07.030551 | Free, Freely available | https://github.com/chanzuckerberg/idseq-workflows/wiki | SCR_019038 | Infectious Disease Sequencing Platform, IDseq Portal | 2025-05-12 11:20:34 | 18 | |||||||
|
CLIP Tool Kit Resource Report Resource Website 10+ mentions |
CLIP Tool Kit (RRID:SCR_019034) | CTK | data processing software, software application, software toolkit, software resource, data analysis software | Software package that provides set of tools for analysis of CLIP data starting from raw reads generated by sequencer. | CLIP data, data analysis, raw reads, sequencer data generation, genome assemblies, data | has parent organization: Columbia University; New York; USA | Free, Available for download, Freely available | SCR_019034 | 2025-05-12 11:20:34 | 22 | |||||||||
|
NEMAR Resource Report Resource Website 1+ mentions |
NEMAR (RRID:SCR_019100) | topical portal, portal, data or information resource | Portal for human electrophysiological data, supports, sharing and in depth analysis of identified human neuroelectromagnetic brain data including scalp EEG, its magnetic counterpart, MEG, and, intracranial iEEG and ECoG. Open access EEG and MEG data archives, analysis, and visualization. Neuroelectromagnetic data, tools, and compute resource. | Human electrophysiological data, neuroelectromagnetic data, neuroelectromagnetic tools, data archives, data analysis, data visualization, EEG data, MEG data, iEEG data, ECoG data, brain data | is affiliated with: OpenNeuro | NIH | Free, Freely available | SCR_019100 | NEuroelectroMagnetic data Archive and tools Resource | 2025-05-12 11:20:37 | 6 | ||||||||
|
tidyverse Resource Report Resource Website 100+ mentions |
tidyverse (RRID:SCR_019186) | data processing software, software application, software toolkit, software resource, data analysis software | Software tool as collection of R packages designed for data science which share underlying design philosophy, grammar, and data structures. Packages work in harmony because they share common data representations and API design. Used in everyday data analyses. | data science, R package, data analysis, common data representation |
uses: ggplot2 uses: dplyr uses: tidyr is used by: tidySingleCellExperiment is used by: microViz is listed by: CRAN |
Free, Available for download, Freely available | https://www.tidyverse.org/ https://github.com/tidyverse/tidyverse |
SCR_019186 | tidyverse 1.3.0 | 2025-05-12 11:20:41 | 145 | ||||||||
|
NiiStat Resource Report Resource Website 50+ mentions |
NiiStat (RRID:SCR_014152) | data processing software, source code, software application, software resource, data analysis software | A set of Matlab scripts for analyzing neuroimaging data from clinical populations. The NiiStat tools are designed to correlate behavioral data (task performance) with brain imaging data. | matlab script, source code, data analysis, neuroimaging data, clinical population |
uses: MATLAB is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Medical University of South Carolina; South Carolina; USA |
Available to the research community | http://www.nitrc.org/plugins/mwiki/index.php/niistat:MainPage | SCR_014152 | 2025-05-12 11:15:22 | 65 | |||||||||
|
COPASI Resource Report Resource Website 100+ mentions |
COPASI (RRID:SCR_014260) | COPASI | standalone software, data processing software, software application, software resource, data analysis software, simulation software | Software application for simulation and analysis of biochemical network models and their dynamics. COPASI supports models in the SBML standard and can simulate their behavior using ODEs or Gillespies stochastic simulation algorithm. Arbitrary discrete events can be included in such simulations. Models in COPASI are based on reactions that convert a set of species into another set of species. Simulation can be performed either with stochastic kinetics or with differential equations. COPASI also includes various methods of analysis and data visualization. | standalone software, simulation software, data analysis, biochemical system simulator, biochemical network model, biochemical network dynamics, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1093/bioinformatics/btl485 | Free, Available for download, Acknowledgement requested | biotools:copasi | https://bio.tools/copasi | SCR_014260 | COPASI: Biochemical System Simulator | 2025-05-12 11:15:26 | 405 | |||||
|
VitalView Software Resource Report Resource Website 10+ mentions |
VitalView Software (RRID:SCR_014497) | data processing software, data acquisition software, software resource, software application, data analytics software | A data acquisition and analysis software program. The program collects data from sensors and receivers and displays graphical data analysis as well as descriptive statistics. | data acquisition, data analysis | PMID:12213503 | Commercial | SCR_014497 | 2025-05-12 11:15:38 | 17 | ||||||||||
|
SigmaGel Software Resource Report Resource Website 100+ mentions |
SigmaGel Software (RRID:SCR_014598) | data analysis software, data processing software, software application, software resource | 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. | gel, gel analysis software, twain, data analysis | Available from SPSS Software | SCR_014598 | SigmaGel | 2025-05-12 11:15:44 | 151 | ||||||||||
|
StatPlus Mac Resource Report Resource Website 100+ mentions |
StatPlus Mac (RRID:SCR_014635) | data analysis software, data processing software, software application, software resource | 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. | statistics, mac, ios, excel, data analysis, software | Available for download | SCR_014635 | StatPlus | 2025-05-12 11:15:47 | 179 | ||||||||||
|
CopyCaller Resource Report Resource Website 100+ mentions |
CopyCaller (RRID:SCR_014486) | data analysis software, data processing software, software application, software resource | 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 | 2025-05-12 11:15:37 | 327 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that RRID has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on RRID then you can log in from here to get additional features in RRID such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into RRID you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
