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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 Authority Synonyms Record Last Update Mentions Count
Enrichr
 
Resource Report
Resource Website
5000+ mentions
Enrichr (RRID:SCR_001575) Enrichr analysis service resource, data analysis service, production service resource, service resource, software application, software resource A web-based gene list enrichment analysis tool that provides various types of visualization summaries of collective functions of gene lists. It includes new gene-set libraries, an alternative approach to rank enriched terms, and various interactive visualization approaches to display enrichment results using the JavaScript library, Data Driven Documents (D3). The software can also be embedded into any tool that performs gene list analysis. System-wide profiling of genes and proteins in mammalian cells produce lists of differentially expressed genes / proteins that need to be further analyzed for their collective functions in order to extract new knowledge. Once unbiased lists of genes or proteins are generated from such experiments, these lists are used as input for computing enrichment with existing lists created from prior knowledge organized into gene-set libraries. bed, gene, software as a service, rna-seq, analyze, protein, function, gene list, visualization, bio.tools is listed by: bio.tools
is listed by: Debian
has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA
PMID:23586463 Free, Freely available biotools:enrichr, SciRes_000171 https://bio.tools/enrichr SCR_001575 SciCrunch Registry 2026-11-07 11:54:21 5047
CisGenome
 
Resource Report
Resource Website
50+ mentions
CisGenome (RRID:SCR_001558) data analysis tool Integrated software tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis. sequencing software, chip seq, downstream analysis, chip analysis, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
works with: TileMap
PMID:18978777 Free, Available for download, Freely available OMICS_00423, biotools:cisgenome https://bio.tools/cisgenome http://biogibbs.stanford.edu/~jihk/CisGenome/index.htm SCR_001558 SciCrunch Registry CisGenome v2.0 2026-11-07 11:54:21 83
DNACLUST
 
Resource Report
Resource Website
1+ mentions
DNACLUST (RRID:SCR_001771) software resource Software program for clustering large number of short similar DNA sequences. It was originally designed for clustering targeted 16S rRNA pyrosequencing reads. cluster, dna sequence, gene, 16s rrna pyrosequencing read, microbiome is listed by: OMICtools
is listed by: Human Microbiome Project
is listed by: Debian
has parent organization: SourceForge
PMID:21718538
DOI:10.1186/1471-2105-12-271
Free, Available for download, Freely available OMICS_01955 https://sources.debian.org/src/dnaclust/ SCR_001771 SciCrunch Registry DNAClust 2026-11-07 11:54:33 9
InterMine
 
Resource Report
Resource Website
10+ mentions
InterMine (RRID:SCR_001772) software resource An open source data warehouse system built for the integration and analysis of complex biological data that enables the creation of biological databases accessed by sophisticated web query tools. Parsers are provided for integrating data from many common biological data sources and formats, and there is a framework for adding data. InterMine includes a user-friendly web interface that works "out of the box" and can be easily customized for specific needs, as well as a powerful, scriptable web-service API to allow programmatic access to data. mac os x, unix/linux, windows, java, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: University of Cambridge; Cambridge; United Kingdom
Wellcome Trust PMID:24753429 Free, Freely available OMICS_03840, biotools:intermine https://github.com/intermine/intermine, https://bio.tools/intermine http://intermine.github.io/intermine.org/ SCR_001772 SciCrunch Registry 2026-11-07 11:54:32 25
An Integrated Multiple Structure Visualization and Multiple Sequence Alignment Application
 
Resource Report
Resource Website
An Integrated Multiple Structure Visualization and Multiple Sequence Alignment Application (RRID:SCR_001646) data analysis software, data processing software, data visualization software, rendering software, software application, software resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Friend is a bioinformatics application designed for simultaneous analysis and visualization of multiple structures and sequences of proteins and/or DNA/RNA. The application provides basic functionalities such as: structure visualization with different rendering and coloring, sequence alignment, and simple phylogeny analysis, along with a number of extended features to perform more complex analyses of sequence structure relationships, including: structural alignment of proteins, investigation of specific interaction motifs, studies of protein-protein and protein-DNA interactions, and protein super-families. Friend is also useful for the functional annotation of proteins, protein modeling, and protein folding studies. Friend provides three levels of usage; 1) an extensive GUI for a scientist with no programming experience, 2) a command line interface for scripting for a scientist with some programming experience, and 3) the ability to extend Friend with user written libraries for an experienced programmer. The application is linked and communicates with local and remote sequence and structure databases. alignment, analysis, bioinformatics, database, dna, interaction, motif, phylogeny, protein, rna, scientist, sequence, structure, super-family, visualization, bio.tools is listed by: bio.tools
is listed by: Debian
has parent organization: Northeastern University; Massachusetts; USA
PMID:16076889 THIS RESOURCE IS NO LONGER IN SERVICE biotools:friend, nif-0000-10149 https://bio.tools/friend SCR_001646 SciCrunch Registry FRIEND 2026-11-07 11:54:32 0
Prediction of Amyloid Structure Aggregation
 
Resource Report
Resource Website
100+ mentions
Prediction of Amyloid Structure Aggregation (RRID:SCR_001768) PASTA analysis service resource, data analysis service, production service resource, service resource, software resource, web application Online interface that utilizes an algorithm to predict the most aggregation-prone portions and the corresponding beta-strand inter-molecular pairing for a given input sequence. Users can paste the sequence into the interface and output the appropriate sequence. protein aggregation, sequence, dna, rna, amyloid structure, protein analysis, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: University of Padua; Padua; Italy
Padova University Progetto di Ateneo CPDA121890;
Italian Ministry for University and Research FIRB Futuro in Ricerca RBFR08ZSXY
PMID:24848016 Free, Freely available biotools:pasta, OMICS_03861 https://bio.tools/pasta SCR_001768 SciCrunch Registry PASTA 2.0, Prediction of amyloid structure aggregation 2026-11-07 11:54:32 180
PLINK
 
Resource Report
Resource Website
10000+ mentions
Issue
PLINK (RRID:SCR_001757) data analysis software, data processing software, software application, software resource, software toolkit Open source whole genome association analysis toolset, designed to perform range of basic, large scale analyses in computationally efficient manner. Used for analysis of genotype/phenotype data. Through integration with gPLINK and Haploview, there is some support for subsequent visualization, annotation and storage of results. PLINK 1.9 is improved and second generation of the software. gene, genetic, genomic, genotype, phenotype, copy number variant, whole-genome association, population, linkage analysis, whole-genome association study, data management, summary statistics, population stratification, association analysis, identity-by-descent estimation is listed by: OMICtools
is listed by: Genetic Analysis Software
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: Debian
is listed by: SoftCite
is related to: Whap
is related to: PLINK/SEQ
is related to: Haploview
is related to: MendelIHT.jl
PMID:17701901
DOI:10.1086/519795
Free, Available for download, Freely Available nlx_154200, OMICS_00206, SCR_021271 https://zzz.bwh.harvard.edu/plink/, https://www.cog-genomics.org/plink/1.9/general_usage#cite, https://sources.debian.org/src/plink/ http://pngu.mgh.harvard.edu/~purcell/plink/ SCR_001757 SciCrunch Registry PLINK 1.9, PLINK/SEQ, plink - Whole genome association analysis toolset 2026-11-07 11:54:33 16581
unifiedWMWqPCR
 
Resource Report
Resource Website
unifiedWMWqPCR (RRID:SCR_001706) software resource Software package that implements the unified Wilcoxon-Mann-Whitney Test for qPCR data. This modified test allows for testing differential expression in qPCR data. standalone software, mac os x, unix/linux, windows, r, gene expression, microtitre plate assay, qpcr, differential expression, multiple comparison, quality control, visualization, qpcr, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: Bioconductor
PMID:24794933 Free, Available for download, Freely available OMICS_03937, biotools:unifiedwmwqpcr https://bio.tools/unifiedwmwqpcr SCR_001706 SciCrunch Registry unifiedWMWqPCR - Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data 2026-11-07 11:54:38 0
CQN
 
Resource Report
Resource Website
1+ mentions
CQN (RRID:SCR_001786) CQN software resource A normalization tool for RNA-Seq data, implementing the conditional quantile normalization method. rna-seq, differential expression, preprocessing, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: Bioconductor
has parent organization: Johns Hopkins Bloomberg School of Public Health; Maryland; USA
PMID:22285995 Free, Available for download, Freely available OMICS_01949, biotools:cqn https://bio.tools/cqn SCR_001786 SciCrunch Registry Conditional Quantile Normalization 2026-11-07 11:54:26 6
MEME Suite - Motif-based sequence analysis tools
 
Resource Report
Resource Website
1000+ mentions
MEME Suite - Motif-based sequence analysis tools (RRID:SCR_001783) MEME Suite analysis service resource, data analysis service, data analysis software, data or information resource, data processing software, database, production service resource, service resource, software application, software resource, source code Suite of motif-based sequence analysis tools to discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences; search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN; compare a motif to all motifs in a database of motifs; associate motifs with Gene Ontology terms via their putative target genes, and analyze motif enrichment using SpaMo or CentriMo. Source code, binaries and a web server are freely available for noncommercial use. gene ontology, motif, comparative genomics, dna regulatory motif, dna sequence, dna, gene, transcription factor, genome, protein, analysis, function analysis, comparison, cluster, enrichment analysis, sequence analysis, bio.tools, FASEB list lists: DREME
is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
is related to: Gene Ontology
is related to: Glam2
is related to: ANNOgesic
is related to: memesuite-lite
has parent organization: National Biomedical Computation Resource
is parent organization of: GOMO - Gene Ontology for Motifs
NCRR R01 RR021692 PMID:19458158
DOI:10.1093/nar/gkl198
Free, Freely available nif-0000-10298, biotools:meme_suite, OMICS_08103 https://bio.tools/meme_suite http://meme.sdsc.edu/meme4_6_1/intro.html, http://meme.nbcr.net/meme/, https://sources.debian.org/src/meme/ SCR_001783 SciCrunch Registry The MEME Suite 2026-11-07 11:54:41 2472
CCAT
 
Resource Report
Resource Website
50+ mentions
CCAT (RRID:SCR_001843) CCAT software resource THIS RESOURCE IS OUT OF SERVICE, documented on April 5, 2017, A software package for the analysis of ChIP-seq data with negative control., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: Genome Institute of Singapore; Singapore; Singapore
PMID:20371496 THIS RESOURCE IS NO LONGER IN SERVICE OMICS_00428, biotools:ccat https://bio.tools/ccat SCR_001843 SciCrunch Registry Control based ChIP-Seq Analysis Tools 2026-11-07 11:54:34 76
GenABEL
 
Resource Report
Resource Website
500+ mentions
GenABEL (RRID:SCR_001842) software library, software resource, software toolkit THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. R software library for genome-wide association analysis for quantitative, binary and time-till-event traits. r, genome-wide association, single nucleotide polymorphism is listed by: OMICtools
is listed by: Genetic Analysis Software
is listed by: Debian
is listed by: SoftCite
Centre for Medical Systems Biology; Netherlands ;
Netherlands Genomics Initiative ;
Netherlands Organisation for Scientific Research ;
Russian Foundation for Basic Research
PMID:17384015
DOI:10.1186/1471-2105-11-134
DOI:10.1093/bioinformatics/btm108
THIS RESOURCE IS NO LONGER IN SERVICE nlx_154328, OMICS_00234 http://mga.bionet.nsc.ru/~yurii/ABEL/GenABEL/, https://cran.r-project.org/web/packages/GenABEL/index.html, https://sources.debian.org/src/probabel/ SCR_001842 SciCrunch Registry GenABEL package, R/GENABEL 2026-11-07 11:54:34 506
FreeSurfer
 
Resource Report
Resource Website
10000+ mentions
FreeSurfer (RRID:SCR_001847) FreeSurfer data processing software, data visualization software, image analysis software, software application, software resource Open source software suite for processing and analyzing human brain MRI images. Used for reconstruction of brain cortical surface from structural MRI data, and overlay of functional MRI data onto reconstructed surface. Contains automatic structural imaging stream for processing cross sectional and longitudinal data. Provides anatomical analysis tools, including: representation of cortical surface between white and gray matter, representation of the pial surface, segmentation of white matter from rest of brain, skull stripping, B1 bias field correction, nonlinear registration of cortical surface of individual with stereotaxic atlas, labeling of regions of cortical surface, statistical analysis of group morphometry differences, and labeling of subcortical brain structures.Operating System: Linux, macOS. processing, analysis, human, brain, MRI, image, reconstruction, cortical, surface, fMRI, data is used by: Wisconsin Cortical Thickness Analysis (CTA) Toolbox
is used by: freesurfR
is used by: Automatic Analysis
is used by: NHP Freesurfer
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC)
is listed by: Biositemaps
is listed by: Debian
is listed by: SoftCite
is related to: PySurfer
is related to: RFT FDR
is related to: FMRLAB
is related to: TRACULA
is related to: BASH4RfMRI
has parent organization: Harvard University; Cambridge; United States
has plug in: JOSA
works with: NIAG Addiction Data
NCRR RR014075;
NCRR U24 RR021382;
NINDS R01 NS052585
PMID:22248573 Free, Available for download, Freely available nif-0000-00304 https://sources.debian.org/src/freesurfer/, http://www.nitrc.org/projects/freesurfer, http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall SCR_001847 SciCrunch Registry 2026-11-07 11:54:34 12664
S-MART
 
Resource Report
Resource Website
10+ mentions
S-MART (RRID:SCR_001908) S-MART software resource Software toolbox that manages your RNA-Seq and ChIP-Seq data and also produces many different plots to visualize your data. It performs several tasks that are usually required during the analysis of mapped RNA-Seq and ChIP-Seq reads, including data selection and data visualization. It includes the selection (or the exclusion) of the data that overlaps with a reference set, clustering and comparative analysis. It also provides many ways to visualize data: size of the reads, density on the genome, distance with respect to a reference set, and the correlation of two data sets (with cloud plots). A computer science background is not required to run it through a graphical interface and it can be run on any personal computer, yielding results within an hour for most queries. high throughput sequencing, rna-seq, chip-seq, python, linux, ms windows, mac, short-read, selection, visualization, bio.tools, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
PMID:21998740 Free, Available for download, Freely available OMICS_01937, biotools:mapperanalyzer, biotools:s-mart https://bio.tools/s-mart, https://bio.tools/mapperanalyzer SCR_001908 SciCrunch Registry 2026-11-07 11:54:36 24
SamSPECTRAL
 
Resource Report
Resource Website
1+ mentions
SamSPECTRAL (RRID:SCR_001858) software resource Software that identifies cell population in flow cytometry data. It demonstrates significant advantages in proper identification of populations with non-elliptical shapes, low density populations close to dense ones, minor subpopulations of a major population and rare populations. It samples large data such that spectral clustering is possible while preserving density information in edge weights. More specifically, given a matrix of coordinates as input, SamSPECTRAL first builds the communities to sample the data points. Then, it builds a graph and after weighting the edges by conductance computation, the graph is passed to a classic spectral clustering algorithm to find the spectral clusters. The last stage of SamSPECTRAL is to combine the spectral clusters. The resulting connected components estimate biological cell populations in the data sample. software package, mac os x, unix/linux, windows, r, cell biology, clustering, flow cytometry, stem cell, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: Bioconductor
Cancer, HIV PMID:20667133 Free, Available for download, Freely available OMICS_05638, biotools:samspectral https://bio.tools/samspectral SCR_001858 SciCrunch Registry SamSPECTRAL - Identifies cell population in flow cytometry data 2026-11-07 11:54:27 4
SHARCGS
 
Resource Report
Resource Website
1+ mentions
SHARCGS (RRID:SCR_002026) data analysis software, data processing software, sequence analysis software, software application, software resource Software package for a DNA assembly program designed for de novo assembly of 25-40mer input fragments and deep sequence coverage. dna, assembly, de novo, rna, sequencing, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: Max Planck Institute for Molecular Genetics; Berlin; Germany
PMID:17908823 Free, Available for download, Freely available OMICS_00029, biotools:sharcgs https://bio.tools/sharcgs SCR_002026 SciCrunch Registry SHort read Assembler based on Robust Contig extension for Genome Sequencing (SHARCGS), SHARCGS - SHort read Assembler based on Robust Contig extension for Genome Sequencing, SHort read Assembler based on Robust Contig extension for Genome Sequencing 2026-11-07 11:54:36 4
SHORTY
 
Resource Report
Resource Website
1+ mentions
SHORTY (RRID:SCR_002048) data analysis software, data processing software, sequence analysis software, software application, software resource Software for targeted de novo assembly of microreads with mate pair information and sequencing errors. sequencing, dna, de novo, microreads, assembler, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
PMID:19208115 Free, Available for download, Freely available biotools:shorty, OMICS_00030 https://bio.tools/shorty SCR_002048 SciCrunch Registry 2026-11-07 11:54:50 3
ASPGD
 
Resource Report
Resource Website
100+ mentions
ASPGD (RRID:SCR_002047) ASPGD, ASPGD LOCUS, ASPGD REF data or information resource, data repository, database, service resource, storage service resource Database of genetic and molecular biological information about the filamentous fungi of the genus Aspergillus including information about genes and proteins of Aspergillus nidulans and Aspergillus fumigatus; descriptions and classifications of their biological roles, molecular functions, and subcellular localizations; gene, protein, and chromosome sequence information; tools for analysis and comparison of sequences; and links to literature information; as well as a multispecies comparative genomics browser tool (Sybil) for exploration of orthology and synteny across multiple sequenced Sgenus species. Also available are Gene Ontology (GO) and community resources. Based on the Candida Genome Database, the Aspergillus Genome Database is a resource for genomic sequence data and gene and protein information for Aspergilli. Among its many species, the genus contains an excellent model organism (A. nidulans, or its teleomorph Emericella nidulans), an important pathogen of the immunocompromised (A. fumigatus), an agriculturally important toxin producer (A. flavus), and two species used in industrial processes (A. niger and A. oryzae). Search options allow you to: *Search AspGD database using keywords. *Find chromosomal features that match specific properties or annotations. *Find AspGD web pages using keywords located on the page. *Find information on one gene from many databases. *Search for keywords related to a phenotype (e.g., conidiation), an allele (such as veA1), or an experimental condition (e.g., light). Analysis and Tools allow you to: *Find similarities between a sequence of interest and Aspergillus DNA or protein sequences. *Display and analyze an Aspergillus sequence (or other sequence) in many ways. *Navigate the chromosomes set. View nucleotide and protein sequence. *Find short DNA/protein sequence matches in Aspergillus. *Design sequencing and PCR primers for Aspergillus or other input sequences. *Display the restriction map for a Aspergillus or other input sequence. *Find similarities between a sequence of interest and fungal nucleotide or protein sequences. AspGD welcomes data submissions. function, gene, gene name, annotation, aspergillus, aspergillus nidulans, chromosome, community, dna, genome, genomic, localization, orthology, phenotype, protein, protein-coding genes, s. cerevisiae, sequence, allele, data analysis service, bio.tools, FASEB list is used by: NIF Data Federation
is listed by: bio.tools
is listed by: Debian
is related to: Candida Genome Database
is related to: AmiGO
has parent organization: Stanford University School of Medicine; California; USA
has parent organization: Broad Institute
NIAID R01 AI077599 PMID:19773420 THIS RESOURCE IS NO LONGER IN SERVICE nif-0000-12244, biotools:aspgd http://www.aspergillusgenome.org/, https://bio.tools/aspgd SCR_002047 SciCrunch Registry Aspergillus Genome Database, ASPGD REF, ASPGD LOCUS 2026-11-07 11:54:31 218
ADaCGH2
 
Resource Report
Resource Website
ADaCGH2 (RRID:SCR_001981) software resource Software for analysis and plotting of array comparative genomic hybridization (CGH) data. It allows usage of Circular Binary Segementation, wavelet-based smoothing (both as in Liu et al., and HaarSeg as in Ben-Yaacov and Eldar), HMM, BioHMM, GLAD, CGHseg. Most computations are parallelized (either via forking or with clusters, including MPI and sockets clusters) and use ff for storing data. standalone software, mac os x, unix/linux, windows, r, copy number variant, microarray, bio.tools is listed by: OMICtools
is listed by: bio.tools
is listed by: Debian
has parent organization: Bioconductor
PMID:24532724 Free, Available for download, Freely available biotools:adacgh2, OMICS_03697 https://bio.tools/adacgh2 SCR_001981 SciCrunch Registry ADaCGH2 - Analysis of big data from aCGH experiments using parallel computing and ff objects 2026-11-07 11:54:38 0
Pathway Commons
 
Resource Report
Resource Website
10+ mentions
Pathway Commons (RRID:SCR_002103) PC data access protocol, data or information resource, database, software resource, web service Database of publicly available pathways from multiple organisms and multiple sources represented in a common language. Pathways include biochemical reactions, complex assembly, transport and catalysis events, and physical interactions involving proteins, DNA, RNA, small molecules and complexes. Pathways were downloaded directly from source databases. Each source pathway database has been created differently, some by manual extraction of pathway information from the literature and some by computational prediction. Pathway Commons provides a filtering mechanism to allow the user to view only chosen subsets of information, such as only the manually curated subset. The quality of Pathway Commons pathways is dependent on the quality of the pathways from source databases. Pathway Commons aims to collect and integrate all public pathway data available in standard formats. It currently contains data from nine databases with over 1,668 pathways, 442,182 interactions,414 organisms and will be continually expanded and updated. (April 2013) biological pathway, pathway, molecule, biopax, standard exchange format, bio.tools is listed by: bio.tools
is listed by: Debian
is listed by: SoftCite
is related to: cPath
is related to: Biological General Repository for Interaction Datasets (BioGRID)
is related to: IntAct
is related to: Reactome
is related to: MINT
is related to: HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism
is related to: Cancer Cell Map
is related to: HPRD - Human Protein Reference Database
is related to: Integrated Molecular Interaction Database
is related to: Pathway Interaction Database
is related to: CHEBI
is related to: UniProt
is related to: PANTHER
is related to: WebGestalt: WEB-based GEne SeT AnaLysis Toolkit
has parent organization: University of Toronto; Ontario; Canada
NHGRI P41HG004118;
NIGMS 2R01GM070743-06;
NIGMS 1T32 GM083937;
Cancer Biomedical Informatics Grid
PMID:21071392 Free, Freely available nif-0000-20884, r3d100012731, biotools:PathwayCommons_web_service_API https://bio.tools/PathwayCommons_web_service_API SCR_002103 SciCrunch Registry 2026-11-07 11:54:51 14

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