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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.

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Resource Name Proper Citation Abbreviations Resource Type Description Keywords Resource Relationships Related Condition Funding Defining Citation Availability Specification URL Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
University of Miami Hussman Institute for Human Genomics Genotyping Core Facility
 
Resource Report
Resource Website
1+ mentions
University of Miami Hussman Institute for Human Genomics Genotyping Core Facility (RRID:SCR_017820) access service resource, service resource, core facility Core provides services in analyzing genetic variation, performing genome-wide association studies, conducting non-human genotyping. Offers flexible platforms from low to high throughput, tailored to research needs. Specializes in Illumina Genotyping Arrays and TaqMan Allelic Discrimination Assays, with fully automated processing using Tecan EVOs and BioMek liquid handlers and Genologics LIMS for reliable data tracking.Applications include: GWAS – Identify genetic variants linked to traits and diseases; PRS Analysis – Assess genetic risk for complex diseases; Pharmacogenomics – Study genetic factors in drug response; Population Genetics – Explore ancestry and genetic diversity; CNV Analysis – Detect large-scale genomic variations; Methylation Analysis. Genotyping, data, analysis, epigenetics, methylation, sequencing, ABRF is listed by: ABRF CoreMarketplace
has parent organization: University of Miami Miller School of Medicine; Florida; USA
Open ABRF_596 https://coremarketplace.org/?FacilityID=596&citation=1 SCR_017820 , Genotyping at the CGT, University of Miami Miller School of Medicine Genotyping Core Facility 2026-07-28 09:44:43 1
Scripps Research Institute - Florida Flow Cytometry Core Facility
 
Resource Report
Resource Website
Scripps Research Institute - Florida Flow Cytometry Core Facility (RRID:SCR_017830) access service resource, service resource, core facility Flow cytometry core to measure phenotypic, biochemical and molecular characteristics of individual cells or particles suspended in fluid stream.Flow Cytometry Core on Jupiter, Florida campus of Scripps Research provides services including Cell Sorting, Analytical Cytometry,Data Analysis,Microdissection and Imaging. Hematology services including:Cell Sorting on ARIA: violet, blue, green and red lasers and on FUSION: violet, blue, green and red lasers; Cell Analysis on LSR2: ultra-violet, violet, blue, green and red lasers, GALLIOS: violet, blue, green and red lasers,CANTO: violet, blue and red lasers;Laser Microdissection and Fluorescence Imaging using LEICA LMD 7000;Hematology using HEMAVET 950FS. Flow, cytometry, phenotypic, cell, particle, sorting, data, analysis, microdissection, imaging, hematology, service, core, ABRF is listed by: ABRF CoreMarketplace Open ABRF_615 SCR_017830 Flow Cytometry 2026-07-28 09:44:34 0
Biocode Commons
 
Resource Report
Resource Website
Biocode Commons (RRID:SCR_024553) data or information resource, topical portal, portal Platform provides resources for genomic observations from collection to analysis and publication. Works with standards community to ensure clear vocabularies and useful ontologies for biological resources and related assets. Biocode Commons is also collaborating on development of Biological Collections Ontology, working to better integrate ontologies, vocabularies, and relevant standards that are related to BCO. Biological Collections Ontology, Biological Collections Ontology development, genomic observations, collection, analysis, publication, standards community, is listed by: DataCite
is listed by: University of California; California; USA
has parent organization: University of California; California; USA
Free, Freely available https://api.datacite.org/dois?prefix=10.7286 SCR_024553 2026-07-28 09:46:07 0
DPARSF
 
Resource Report
Resource Website
500+ mentions
DPARSF (RRID:SCR_002372) DPARSF software application, software toolkit, software resource, data processing software A MATLAB toolbox forpipeline data analysis of resting-state fMRI that is based on Statistical Parametric Mapping (SPM) and a plug-in software within DPABI. After the user arranges the Digital Imaging and Communications in Medicine (DICOM) files and click a few buttons to set parameters, DPARSF will then give all the preprocessed (slice timing, realign, normalize, smooth) data and results for functional connectivity, regional homogeneity, amplitude of low-frequency fluctuation (ALFF), fractional ALFF, degree centrality, voxel-mirrored homotopic connectivity (VMHC) results. DPARSF can also create a report for excluding subjects with excessive head motion and generate a set of pictures for easily checking the effect of normalization. In addition, users can also use DPARSF to extract time courses from regions of interest. DPARSF basic edition is very easy to use while DPARSF advanced edition (alias: DPARSFA) is much more flexible and powerful. DPARSFA can parallel the computation for each subject, and can be used to reorient images interactively or define regions of interest interactively. Users can skip or combine the processing steps in DPARSF advanced edition freely. magnetic resonance, fmri, resting-state fmri, matlab, analysis, brain is used by: DPABI
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
has parent organization: Beijing Normal University; Beijing; China
has parent organization: RFMRI.ORG
PMID:20577591 GNU General Public License nlx_155735 http://www.nitrc.org/projects/dparsf SCR_002372 Data Processing Assistant for Resting-State fMRI 2026-07-28 09:40:36 564
Fusion ICA Toolbox
 
Resource Report
Resource Website
10+ mentions
Fusion ICA Toolbox (RRID:SCR_003494) FIT software application, software toolkit, software resource, data processing software A MATLAB toolbox which implements the joint Independent Component Analysis (ICA), parallel ICA and CCA with joint ICA methods. It is used to to extract the shared information across modalities like fMRI, EEG, sMRI and SNP data. * Environment: Win32 (MS Windows), Gnome, KDE * Operating System: MacOS, Windows, Linux * Programming Language: MATLAB * Supported Data Format: ANALYZE, NIfTI-1 analysis, functional magnetic resonance imaging, cca, image, eeg, neuroimaging, matlab, smri, snp, mri, algorithm, reusable library, independent component analysis, principal component analysis is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: Biositemaps
has parent organization: University of New Mexico; New Mexico; USA
NIBIB 1RO1EB005846;
NSF 0612076
GNU General Public License nif-0000-36743 http://www.nitrc.org/projects/fit SCR_003494 Fusion ICA Toolbox (FIT) 2026-07-28 09:40:48 13
Bern-Barcelona EEG database
 
Resource Report
Resource Website
1+ mentions
Bern-Barcelona EEG database (RRID:SCR_001582) Bern-Barcelona EEG database data or information resource, data set, source code, software resource THIS RESOURCE IS NO LONGER IN SERVICE, documented November 23, 2020; EEG data set, source code, and results from 7500 signal pairs from 5 epilepsy patients analyzed in the manuscript, Andrzejak RG, Schindler K, Rummel C. Nonrandomness, nonlinear dependence, and nonstationarity of electroencephalographic recordings from epilepsy patients. Phys. Rev. E, 86, 046206, 2012. All Matlab source codes are included in the file ASR_Sources_2012_10_16.zip. The clinical purpose of these recordings was to delineate the brain areas to be surgically removed in each individual patient in order to achieve seizure control. eeg, electroencephalogram, epilepsy, intracranial, eeg recording, signal, analysis, time series, nonlinear, surrogate signal, surrogate, matlab, focal, non-focal, signal has parent organization: Pompeu Fabra University; Barcelona; Spain Epilepsy, Pharmacoresistant focal-onset epilepsy, Seizure Spanish Ministry of Education and Science grant FIS-2010-18204;
Swiss National Science Foundation SNF 320030-122010;
Swiss National Science Foundation SNF 33CM30-124089
PMID:23214662 Free, Available for download, Freely available nlx_153819 http://ntsa.upf.edu/downloads/andrzejak-rg-schindler-k-rummel-c-2012-nonrandomness-nonlinear-dependence-and, http://www.dtic.upf.edu/~ralph/sc/ SCR_001582 2026-07-28 09:40:19 3
Gene Expression Omnibus (GEO)
 
Resource Report
Resource Website
10000+ mentions
Gene Expression Omnibus (GEO) (RRID:SCR_005012) GEO service resource, data or information resource, data repository, database, storage service resource Functional genomics data repository supporting MIAME-compliant data submissions. Includes microarray-based experiments measuring the abundance of mRNA, genomic DNA, and protein molecules, as well as non-array-based technologies such as serial analysis of gene expression (SAGE) and mass spectrometry proteomic technology. Array- and sequence-based data are accepted. Collection of curated gene expression DataSets, as well as original Series and Platform records. The database can be searched using keywords, organism, DataSet type and authors. DataSet records contain additional resources including cluster tools and differential expression queries. gold standard, genomics, data, repository, microarray, mRNA, DNA, protein, analysis, SAGE, mass spectrometry, dataset is used by: ChIPseeker
is recommended by: National Library of Medicine
is recommended by: NIDDK Information Network (dkNET)
is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases
is related to: Allen Institute for Brain Science
has parent organization: NCBI
works with: shinyGEO
works with: Drug Gene Budger
works with: Signaling Pathways Project
works with: GEN3VA
National Library of Medicine PMID:23193258
PMID:21097893
PMID:18940857
PMID:17160034
PMID:17099226
PMID:16939800
PMID:16888359
PMID:15608262
PMID:11752295
r3d100010283, nif-0000-00142, nlx_96903, OMICS_01030, SCR_007303 http://www.ncbi.nlm.nih.gov/sites/entrez?db=gds, http://www.ncbi.nlm.nih.gov/geo/, https://doi.org/10.17616/R33P44 http://www.ncbi.nlm.nih.gov/gds SCR_005012 Gene Expression Omnibus (GEO), Entrez GEO DataSets, Gene Expression Data Sets, Gene Expression Omnibus, GEO, NCBI GEO DataSets, GEO DataSets, Gene Expression Omnibus DataSets 2026-07-28 09:41:08 11944
SPM
 
Resource Report
Resource Website
5000+ mentions
Issue
SPM (RRID:SCR_007037) SPM software application, data analysis software, software resource, data processing software, image analysis software Software package for analysis of brain imaging data sequences. Sequences can be a series of images from different cohorts, or time-series from same subject. Current release is designed for analysis of fMRI, PET, SPECT, EEG and MEG. analysis, brain, imaging, data, sequence, fMRI, PET, SPECT, EEG, MEG, bio.tools uses: Neuroimaging Data Model
uses: imcalc: SPM batch image calculator
is used by: rsfMRI_fconn calculation
is used by: Automatic Analysis
is used by: auto_acpc_reorient
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: 3DVC
is listed by: Debian
is listed by: bio.tools
is listed by: SoftCite
is affiliated with: Clinical Toolbox for SPM
is affiliated with: Statistical non-Parametric Mapping
is related to: WFU Biological Parametric Mapping Toolbox
is related to: vis: SPM Visualized Statistics toolbox
is related to: LEAD-DBS
is related to: CCHMC Pediatric Brain Templates
is related to: IBMA toolbox
is related to: ArtRepair for robust fMRI
is related to: ASL data processing tool box
is related to: BrainVISA / Anatomist
is related to: MRIcro Software
is related to: xjView: A Viewing Program For SPM
is related to: BrainMagix SPM Viewer
is related to: MarsBaR region of interest toolbox for SPM
is related to: NIRS-SPM
is related to: SPM SS - fMRI functional localizers
is related to: Wisconsin White Matter Hyperintensities Segmentation Toolbox
is related to: Dementia-specific FDG PET Template for SPM analyses
is related to: SPM Anatomy Toolbox
is related to: MIPAV: Medical Image Processing and Visualization
is related to: MATLAB
is related to: hMRI-toolbox
is related to: Sandwich Estimator Toolbox
has parent organization: University College London; London; United Kingdom
is required by: MRTool
provides: TSDiffAna
has plug in: ICN_Atlas
works with: UManitoba - JHU Functionally Defined Human White Matter Atlas
works with: NIAG Addiction Data
works with: ICN_Atlas
works with: spm_auto_reorient_coregister
works with: Computational Anatomy Toolbox for SPM
works with: FieldTrip
works with: POAS4SPM
Free, Available for download, Freely available biotools:SPM https://github.com/spm/spm12, https://bio.tools/SPM https://www.fil.ion.ucl.ac.uk/spm/ SCR_007037 Statistical Parametric Mapping, SPM5, SPM2, SPM12, Statistical Parametric Mapping Software, SPM99, SPM8, SPM, SPM96 2026-07-28 09:41:40 8694
Onto-Compare
 
Resource Report
Resource Website
1+ mentions
Onto-Compare (RRID:SCR_005669) Onto-Compare service resource, data or information resource, data analysis service, database, production service resource, analysis service resource Microarrays are at the center of a revolution in biotechnology, allowing researchers to screen tens of thousands of genes simultaneously. Typically, they have been used in exploratory research to help formulate hypotheses. In most cases, this phase is followed by a more focused, hypothesis driven stage in which certain specific biological processes and pathways are thought to be involved. Since a single biological process can still involve hundreds of genes, microarrays are still the preferred approach as proven by the availability of focused arrays from several manufacturers. Since focused arrays from different manufacturers use different sets of genes, each array will represent any given regulatory pathway to a different extent. We argue that a functional analysis of the arrays available should be the most important criterion used in the array selection. We developed Onto-Compare as a database that can provide this functionality, based on the GO nomenclature. Compare commercially available microarrays based on GO. User account required. Platform: Online tool microarray, gene, ontology, gene expression, data-mining, browser, visualization, analysis, compare, search engine, ontology or annotation browser, ontology or annotation search engine, ontology or annotation visualization, database or data warehouse, other analysis, compare commercially available microarrays based on go is listed by: Gene Ontology Tools
is related to: Gene Ontology
has parent organization: Wayne State University; Michigan; USA
PMID:12664686
PMID:15215428
Free for academic use nlx_149108 SCR_005669 2026-07-28 09:41:18 1
Chem Service, Inc.
 
Resource Report
Resource Website
10+ mentions
Chem Service, Inc. (RRID:SCR_008380) material service resource, service resource, production service resource, instrument manufacture Chem Service, Inc. offers the convenience, cost savings and reliability of 1,000 Certified Standards Grade Organic Chemicals at your fingertips with our Organic Mini Stockroom Kit. Whether your lab is big or small, disposal fees are a concern. The Organic Mini-stockroom offers you the ability to have 1000 different chemicals at quantities ranging from 100mg to 10gm; thus, reducing disposal costs. Over 95% of their neat Standards Grade materials have a purity of 98.0% or greater, and have been analyzed by three or more (where feasible) independent methods of analysis. These do not require purity corrections when preparing a solution for use with EPA methods. Their more than 13,000 organic and inorganic standards, and solutions, support EPA Methods, ASTM Methods, State UST Methods, Air monitoring Methods, and International Methods. They offer explosive residue standards, PCB congeners, petroleum hydrocarbon standards for the petrochemical industry, pesticide standards, FAME, and vitamin standards for food analysis. Suited for identification of unknowns, product screening, optimal chemical selection and small scale chemical reactions, the O-1000A Organic Ministockroom Kit was designed for laboratories with broad chemical classification and indentification needs. Chem Service, Inc. is registered by ABS Quality Evaluations, Inc., to the internationally recognized requirements of ISO 9001 for design, development, production, distribution and servicing of organic neat and synthetic reference materials. food, analysis, chemical, industry, method, organic, pestiide, petrochemical, solution, synthetic, vitamin nif-0000-30016 SCR_008380 ChemService 2026-07-28 09:42:19 10
CLC Genomics Workbench
 
Resource Report
Resource Website
100+ mentions
CLC Genomics Workbench (RRID:SCR_011853) software application, data analysis software, software resource, data processing software, data visualization software Commercially available software for visualization and analysis of next generation sequencing data. Used for viewing, exploring, and sharing of NGS analysis results. Complete toolkit for genomics, transcriptomics, epigenomics, and metagenomics in one program. ngs, next, generation, sequencing, gene, rna, visualisation, analysis is listed by: OMICtools
is listed by: SoftCite
works with: CLC Genomics Server
Restricted SCR_016245, OMICS_01124 SCR_011853 2026-07-28 09:42:57 181
Vocal Inventory Clustering Engine (VoICE)
 
Resource Report
Resource Website
1+ mentions
Vocal Inventory Clustering Engine (VoICE) (RRID:SCR_016004) VoICE software application, software resource, data analysis software, data processing software Software that groups vocal elements of birdsong by creating a high dimensionality dataset through scoring spectral similarity between vocalizations. bird, song, birdsong, vocal, audio, analysis, vocalization, spectral similarity, avian, matlab uses: MATLAB Autism Speaks 7657;
UCLA ;
5T32HC00722834 ;
NIMH RO1MH081754;
NICHD P50 HD055784;
NIMH R01 MH081754;
NIMH R01 MH070712
Free, Available for download SCR_016004 VoICE (Vocal Inventory Clustering Engine), Vocal Inventory Clustering Engine (VoICE), VoICE: Vocal Inventory Clustering Engine, VoICE: A semi-automated pipeline for standardizing vocal analysis across models 2026-07-28 09:44:12 1
Computational Structural Biology Toolbox
 
Resource Report
Resource Website
Computational Structural Biology Toolbox (RRID:SCR_016065) CSB software library, software toolkit, software resource Software package as an application framework and a Python class library. It is designed for reading, storing and analyzing biomolecular structures in a variety of formats with rich support for statistical analyses. software, library, Python, reading, storing, analysis, biomolecular, variety, statistical, analysis, bioinformatic is listed by: Debian
is listed by: OMICtools
Deutsche Forschungsgemeinschaft (DFG) grant HA 5918/1-1;
Max Planck Society
PMID:22942023 Free, Available for download OMICS_09827 https://sources.debian.org/src/csb/ SCR_016065 Computational Structural Biology Toolbox (CSB), CSB Toolbox 2026-07-28 09:44:08 0
Seurat
 
Resource Report
Resource Website
5000+ mentions
Seurat (RRID:SCR_016341) software application, data analysis software, software resource, data processing software, software toolkit Software R package designed for QC, analysis, and exploration of single cell RNA-seq data. Enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. Used for quality control, analysis, and exploration of single-cell RNA sequencing (scRNA-seq) data. single, cell, genomic, RNA-seq, data, QC, analysis, source, heterogeneity, transcriptomic, measurement, integrate, diverse is used by: Stardust
is used by: Seurat MapQuery
is related to: DoubletFinder
is related to: Azimuth
works with: SeuratWrappers
works with: Connectome
NHGRI 1DP2HG009623;
NIMH 5R01MH071679;
NSF
PMID:29608179 Free, Available for download, Freely available https://satijalab.org/seurat/get_started.html SCR_016341 2026-07-28 09:44:15 9395
tenx
 
Resource Report
Resource Website
10+ mentions
tenx (RRID:SCR_016957) service resource, data analysis service, software resource, production service resource, analysis service resource, software toolkit Pipeline for the analysis of 10x single cell RNA sequencing data. Collection of python3 pipelines and Rscripts to analyze data generated with the 10x Genomics platform. The pipelines are based on 10x's Cell Ranger pipeline for mapping and quantitation and the R Seurat package for downstream analysis. analysis, 10x, single, cell, RNA, sequencing, data, genomic, platform, mapping, quantitation Free, Available for download, Freely available SCR_016957 2026-07-28 09:44:26 11
Nutil - Neuroimaging utilities
 
Resource Report
Resource Website
10+ mentions
Nutil - Neuroimaging utilities (RRID:SCR_017183) Nutil software application, software toolkit, software resource, data processing software, image processing software, image analysis software Software toolbox to simplify and streamline mechanism of pre and post processing 2D brain image data. Neuroscience image processing and analysis utilities. Stand alone application that runs on all operating systems. Nutil is part of the QUINT workflow. neuroscience, 2D, brain, image, data, processing, analysis is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is related to: Allen Institute for Brain Science
has parent organization: University of Oslo; Oslo; Norway
works with: VisuAlign
European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Framework Partnership Agreement No. 650003 (HBP FPA) and the European Union’s Horizon Europe Programme for Research Infrastructures Grant Agreement No. 101147319 (EBRAINS 2.0). PMID:32973479 Free, Available for download, Freely available https://nutil.readthedocs.io; https://github.com/Neural-Systems-at-UIO/nutil SCR_017183 Neuroimaging utilities 2026-07-28 09:44:27 25
Kids First Data Resource Portal
 
Resource Report
Resource Website
1+ mentions
Kids First Data Resource Portal (RRID:SCR_016493) DRP service resource, disease-related portal, data or information resource, organization portal, data repository, database, topical portal, storage service resource, portal Portal for analysis and interpretation of pediatric genomic and clinical data to advance personalized medicine for detection, therapy, and management of childhood cancer and structural birth defects. For patients, researchers, and clinicians to create centralized database of well curated clinical and genetic sequence data from patients with childhood cancer or structural birth defects. pediatric, genomic, clinical, disease, data, children, cancer, birth, defect, analysis is recommended by: National Library of Medicine pediatric cancer, birth defect the Common Fund’s Gabriella Miller Kids First Pediatric Research Program ;
NIH
Restricted SCR_016553 https://commonfund.nih.gov/kidsfirst, https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001168.v1.p1, https://commonfund.nih.gov/kidsfirst SCR_016493 Data Resource Portal 2026-07-28 09:44:19 3
OrthoFinder
 
Resource Report
Resource Website
1000+ mentions
OrthoFinder (RRID:SCR_017118) software application, software resource, data analysis software, data processing software Software Python application for comparative genomics analysis. Finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of gene duplcation events in those gene trees, infers rooted species tree for species being analysed and maps gene duplication events from gene trees to branches in species tree, improves orthogroup inference accuracy. Runs set of protein sequence files, one per species, in FASTA format. comparative, genomic, analysis, find, orthogroup, ortholog, infer, gene, tree, duplicate, accuracy, protein, sequence, bio.tools is listed by: OMICtools
is listed by: Debian
is listed by: bio.tools
Bill and Melinda Gates Foundation ;
UKAID
PMID:26243257
DOI:10.1101/466201
Free, Available for download, Freely available biotools:OrthoFinder, OMICS_09733, BioTools:OrthoFinder https://bio.tools/OrthoFinder, https://bio.tools/OrthoFinder, https://bio.tools/OrthoFinder SCR_017118 OrthoFinder2, OrthoFinder 2026-07-28 09:44:29 2899
tximport
 
Resource Report
Resource Website
50+ mentions
tximport (RRID:SCR_016752) software application, software resource, data analysis software, data processing software Software R package for importing pseudoaligned reads into R for use with downstream differential expression analysis. Used for import and summarize transcript level estimates for transcript and gene level analysis. pseudoaligned, reads, R, differential, expression, analysis, gene, transcript, bio.tools is listed by: Bioconductor
is listed by: Debian
is listed by: bio.tools
works with: edgeR
works with: DESeq2
SNSF 143883;
European Commission ;
NCI T32 CA009337
DOI:10.12688/f1000research.7563.1 Free, Available for download, Freely available biotools:tximport https://bioconductor.org/packages/tximport/, https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html, https://github.com/F1000Research/tximport, https://bio.tools/tximport https://zenodo.org/record/35123#.W_w3behKiM8 SCR_016752 tximport v1.4.0 2026-07-28 09:44:24 91
Cyflogic
 
Resource Report
Resource Website
10+ mentions
Cyflogic (RRID:SCR_016635) software application, data analysis software, software resource, data processing software, software toolkit Software tool for a flow cytometry data analysis for Microsoft Windows enviroment developed by CyFlo Ltd. Has analysis capabilities, such as dot plot, histogram and statistics. flow, cytometry, data, analysis, CyFlo Ltd., dot, plot, histogram, statistics PMID:23839300 Commercially available, Free for non-commercial research use only and not for use in diagnostic or therapeutic procedures SCR_016635 2026-07-28 09:44:23 25

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