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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 Website Status Alternate IDs Alternate URLs Old URLs Parent Organization Resource ID Synonyms Record Last Update Mentions Count
Arvados
 
Resource Report
Resource Website
1+ mentions
Arvados (RRID:SCR_002223) arvados data repository, storage service resource, service resource Bioinformatics platform for storing, organizing, processing, and sharing genomic and other biomedical big data. Designed to make it easier for bioinformaticians to develop analyses, developers to create genomic web applications and IT administers to manage large-scale compute and storage genomic resources. Designed to run on top of cloud operating systems such as Amazon Web Services and OpenStack. Currently, there are implementations that work on AWS and Xen+Debian/Ubuntu. Functionally, Arvados has two major sets of capabilities: (a) data management and (b) compute management. mapreduce/hadoop, genomic, biomedical, data sharing, compute, data management, cloud is listed by: Debian Free, Freely available OMICS_01835 https://sources.debian.org/src/arvados/ SCR_002223 2026-02-14 02:00:22 3
ARK-Genomics: Centre for Functional Genomics
 
Resource Report
Resource Website
10+ mentions
ARK-Genomics: Centre for Functional Genomics (RRID:SCR_002214) ARK Genomics core facility, portal, data or information resource, organization portal, service resource, access service resource, database Portal for studies of genome structure and genetic variation, gene expression and gene function. Provides services including DNA sequencing of model and non-model genomes using both Next Generation and Sanger sequencing , Gene expression analysis using both microarrays and Next Generation Sequencing, High throughput genotyping of SNP and copy number variants, Data collection and analysis supported in-house high performance computing facilities and expertise, Extensive EST clone collections for a number of animal species, all of commercially available microarray tools from Affymetrix, Illumina, Agilent and Nimblegen, Parentage testing using microsatellites and smaller SNP panels. ARK-Genomics has developed network of researchers whom they support through each stage of their genomics research, from grant application, experimental design and technology selection, performing wet laboratory protocols, through to analysis of data often in conjunction with commercial partners. gene expression, farm, function, gene, genetic, animal, dna, genome, genomic, genotype, knowledge base, model, structure, variation, job, comparative genome hybridization, parentage testing, microsatellite is listed by: ScienceExchange
is related to: Roslin Institute Labs and Facilities
has parent organization: Roslin Institute
works with: University of Edinburgh GenePool Next Generation Sequencing and Bioinformatics
BBSRC Free, Freely available nif-0000-20966, SciEx_157 https://genomics.ed.ac.uk/ SCR_002214 ARK Genomics, Roslin Institute ARK-Genomics 2026-02-14 02:00:20 12
SAMTOOLS
 
Resource Report
Resource Website
10000+ mentions
SAMTOOLS (RRID:SCR_002105) SAMtools sequence analysis software, data processing software, data analysis software, software toolkit, software application, software resource Original SAMTOOLS package has been split into three separate repositories including Samtools, BCFtools and HTSlib. Samtools for manipulating next generation sequencing data used for reading, writing, editing, indexing,viewing nucleotide alignments in SAM,BAM,CRAM format. BCFtools used for reading, writing BCF2,VCF, gVCF files and calling, filtering, summarising SNP and short indel sequence variants. HTSlib used for reading, writing high throughput sequencing data. Samtools, BCFtools, HTSlib, next generation sequencing, nucleotide alignments, sequence variant, genomic, c, perl, read, alignment, nucleotide, sequence, data, process, sam, bam, cram, vcf, bcf, bio.tools is used by: deFuse
is used by: Short Read Sequence Typing for Bacterial Pathogens
is used by: ROSE
is used by: Fcirc
is listed by: OMICtools
is listed by: Genetic Analysis Software
is listed by: SNVer
is listed by: Debian
is listed by: bio.tools
is listed by: SoftCite
is related to: Platypus
is related to: shovill
is related to: pysam
has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom
is parent organization of: SAMtools/BCFtools
is required by: RelocaTE
is required by: Wessim
is required by: SL-quant
is required by: smMIPfil
Wellcome Trust ;
NHGRI U54 HG002750
PMID:19505943
PMID:21903627
DOI:10.1093/bioinformatics/btp352
Free, Available for download, Freely available SCR_018682, biotools:samtools, OMICS_01074, nlx_154607, OMICS_00090 https://github.com/samtools/samtools
https://github.com/samtools/htslib
https://bio.tools/samtools
https://sources.debian.org/src/samtools/
http://samtools.sourceforge.net/ SCR_002105 samtools, Samtools, Sequence Alignment Map TOOLS, SAMtools, SAM tools 2026-02-14 02:00:18 30156
iBIOFind
 
Resource Report
Resource Website
iBIOFind (RRID:SCR_001587) iBIOFind data or information resource, service resource, software application, software resource, database THIS RESOURCE IS NO LONGER IN SERVICE, documented August 17, 2016. C#.NET 4.0 WPF / OWL / REST / JSON / SPARQL multi-threaded, parallel desktop application enables the construction of biomedical knowledge through PubMed, ScienceDirect, EndNote and NIH Grant repositories for tracking the work of medical researchers for ranking and recommendations. Users can crawl web sites, build latent semantic indices to generate literature searches for both Clinical Translation Science Award and non-CTSA institutions, examine publications, build Bayesian networks for neural correlates, gene to gene interactions, protein to protein interactions and as well drug treatment hypotheses. Furthermore, one can easily access potential researcher information, monitor and evolve their networks and search for possible collaborators and software tools for creating biomedical informatics products. The application is designed to work with the ModelMaker, R, Neural Maestro, Lucene, EndNote and MindGenius applications to improve the quality and quantity of medical research. iBIOFind interfaces with both eNeoTutor and ModelMaker 2013 Web Services Implementation in .NET for eNeoTutor to aid instructors to build neuroscience courses as well as rare diseases. Added: Rare Disease Explorer: The Visualization of Rare Disease, Gene and Protein Networks application module. Cinematics for the Image Finder from Yale. The ability to automatically generate and update websites for rare diseases. Cytoscape integration for the construction and visualization of pathways for Molecular targets of Model Organisms. Productivity metrics for medical researchers in rare diseases. iBIOFind 2013 database now includes over 150 medical schools in the US along with Clinical Translational Science Award Institutions for the generation of biomedical knowledge, biomedical informatics and Researcher Profiles. workflow, model, prediction, research trend, rare disease, resource discovery, biomedicine, genomic, neural network, visualization, reporting, search engine, genetic, neural, clinical translation science award, biomedical resource, funding, gene, protein, neuron, collaborator, publication, trend, grant, funding opportunity, report is related to: ModelMaker
is related to: Neural Maestro
is related to: eNeoTutor
is related to: Cytoscape
is related to: Biomedical Resource Ontology
is related to: PubMed
has parent organization: The Cromwell Workshop
THIS RESOURCE IS NO LONGER IN SERVICE nlx_153829 SCR_001587 2026-02-14 02:00:12 0
PLINK
 
Resource Report
Resource Website
10000+ mentions
Issue
PLINK (RRID:SCR_001757) data processing software, data analysis software, software toolkit, software application, software resource 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 PLINK 1.9, PLINK/SEQ, plink - Whole genome association analysis toolset 2026-02-14 02:00:10 15344
Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Bioinformatics Resource
 
Resource Report
Resource Website
Fred Hutchinson Cancer Research Center Co-operative Center for Excellence in Hematology Bioinformatics Resource (RRID:SCR_015324) core facility, analysis service resource, data or information resource, production service resource, service resource, access service resource THIS RESOURCE IS NO LONGER IN SERVICE.Documented on July 27,2022. Core provides bioinformatics specialists available to assist researchers with processing, exploring, and understanding genomics data. hematology, bioinformatics, explore, understand, genomic, data, cancer is listed by: NIDDK Information Network (dkNET)
has parent organization: Fred Hutchinson Cancer Center
Cancer NIDDK P30 DK056465 THIS RESOURCE IS NO LONGER IN SERVICE SCR_015907 SCR_015324 Hutch, Bioinformatic Resource, Fred, Co-operative Center for Excellence in Hematology, Cancer Center 2026-02-14 02:02:50 0
SnpHub
 
Resource Report
Resource Website
1+ mentions
SnpHub (RRID:SCR_018177) software resource, web application Web Shiny-based server framework for retrieving, analyzing and visualizing large genomic variations data. Genomic, data, data visualization, data analysis, data retrieving, bio.tools is listed by: Debian
is listed by: bio.tools
National Natural Science Foundation of China 31701415;
National Key Research and Development Program of China 2018YFD0100803;
National Key Research and Development Program of China 2016YFD0100801
Free, Available for download, Freely available biotools:SnpHub http://guoweilong.github.io/SnpHub/
https://bio.tools/SnpHub
SCR_018177 2026-02-14 02:03:34 1
genomics resource for animal lectins
 
Resource Report
Resource Website
1+ mentions
genomics resource for animal lectins (RRID:SCR_018122) data or information resource, portal, topical portal Resource presents information about animal lectins involved in various sugar recognition processes. Genomic, animal lectin, sugar recognition process has parent organization: Imperial College London; London; United Kingdom BBSRC ;
Wellcome Trust ;
Consortium for Functional Glycomics
Free, Freely available SCR_018122 2026-02-14 02:03:31 3
Q Squared Solutions Expression Analysis
 
Resource Report
Resource Website
1+ mentions
Q Squared Solutions Expression Analysis (RRID:SCR_012497) Q2 Solutions, EA, Q squared solutions, Q2, Q squared core facility, access service resource, service resource, commercial organization Core provides whole genome to focused set gene expression and genotyping assays along with DNA sequencings services, sequence enrichment technologies and bioinformatics support. Platforms utilized include Affymetrix GeneChip, Agilent Sure Select, Fluidigm Access Arrays, Illumina BeadChip, iScan, Genome Analyzer and Hi-Seq, RainDance Technologies RDT 1000 and, the Pacific Biosciences PacBio RS. Expression Analysis offers solutions for challenging specimens such as whole blood and FFPE tissues, as well as nucleic acid isolation and data analysis services. genomic, genotyping, DNA sequencing, is listed by: ScienceExchange
has parent organization: Quintiles
Available to external user SciEx_366 http://www.scienceexchange.com/facilities/expression-analysis SCR_012497 Q2 Solutions Expression Analysis, Q 2 Solutions Expression Analysis, Q 2 Expression Analysis 2026-02-14 02:02:41 1
Virus Pathogen Resource (ViPR)
 
Resource Report
Resource Website
100+ mentions
Virus Pathogen Resource (ViPR) (RRID:SCR_012983) ViPR data visualization software, data repository, storage service resource, data processing software, data or information resource, service resource, software application, software resource, database Provides searchable public repository of genomic, proteomic and other research data for different strains of pathogenic viruses along with suite of tools for analyzing data. Data can be shared, aggregated, analyzed using ViPR tools, and downloaded for local analysis. ViPR is an NIAID-funded resource that support the research of viral pathogens in the NIAID Category A-C Priority Pathogen lists and those causing (re)emerging infectious diseases. It provides a dedicated gateway to SARS-CoV-2 data that integrates data from external sources (GenBank, UniProt, Immune Epitope Database, Protein Data Bank), direct submissions, analysis pipelines and expert curation, and provides a suite of bioinformatics analysis and visualization tools for virology research. flu, gene, bioinformatic, database, diagnostic, genomic, health, human, influenza, pathogen, protein, research, strain, therapeutic, tool, vaccine, virus, visualization, FASEB list is recommended by: National Library of Medicine
is listed by: Data and Computational Resources to Address COVID-19
is listed by: DataCite
is listed by: re3data.org
is listed by: FAIRsharing
has parent organization: University of Texas Southwestern Medical Center; Texas; USA
COVID-19 NIAID Restricted nif-0000-25312, DOI:10.35083, DOI:10.35084, DOI:10.17616/R30P93, DOI:10.25504/FAIRsharing.2qx8n8 http://www.viprbrc.org/
https://doi.org/10.17616/r30p93
https://doi.org/10.35083/
https://doi.org/10.35084/
https://dx.doi.org/10.35083/
https://dx.doi.org/10.35084/
https://fairsharing.org/10.25504/FAIRsharing.2qx8n8
SCR_012983 Virus Pathogen Resource, ViPR 2026-02-14 02:02:25 140
PIAGE
 
Resource Report
Resource Website
PIAGE (RRID:SCR_013124) software resource, software application THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. Software program that performs estimation of power and sample sizes required to detect genetic and environmental main, as well as gene-environment interaction (GxE) effects in indirect matched case-control studies (1:1 matching). When the hypothesis of GxE is tested, power/sample size will be estimated for the detection of GxE, as well as for the detection of genetic and environmental marginal effects. Furthermore, power estimation is implemented for the joint test of genetic marginal and GxE effects (Kraft P et al., 2007). Power and sample size estimations are based on Gauderman''s (2002) asymptotic approach for power and sample size estimations in direct studies of GxE. Hardy-Weinberg equilibrium and independence of genotypes and environmental exposures in the population are assumed. The estimates are based on genotypic codes (G=1 (G=0) for individuals who carry a (non-) risk genotype), which depend on the mode of inheritance (dominant, recessive, or multiplicative). A conditional logistic regression approach is used, which employs a likelihood-ratio test with respect to a biallelic candidate SNP, a binary environmental factor (E=1 (E=0) in (un)exposed individuals), and the interaction between these components. (entry from Genetic Analysis Software) gene, genetic, genomic, r, ms-windows, linux is listed by: Genetic Analysis Software THIS RESOURCE IS NO LONGER IN SERVICE nlx_154534, SCR_009372, nlx_154594 SCR_013124 R/PIAGE, Power of Indirect Association Studies of Gene-Environment Interactions 2026-02-14 02:02:50 0
BOOST
 
Resource Report
Resource Website
10+ mentions
BOOST (RRID:SCR_013133) BOOST software resource, data analysis software, data processing software, software application Software application (entry from Genetic Analysis Software) for a method for detecting gene-gene interactions. It allows examining all pairwise interactions in genome-wide case-control studies. gene, genetic, genomic, logistic regression model, gene-gene interactions is listed by: Genetic Analysis Software Free, Available for download nlx_154249 SCR_013133 BOolean Operation based Screening and Testing 2026-02-14 02:02:22 32
PlasmoDB
 
Resource Report
Resource Website
1000+ mentions
PlasmoDB (RRID:SCR_013331) data repository, storage service resource, web service, data analysis service, analysis service resource, data or information resource, production service resource, service resource, data access protocol, software resource, database Functional genomic database for malaria parasites. Database for Plasmodium spp. Provides resource for data analysis and visualization in gene-by-gene or genome-wide scale. PlasmoDB 5.5 contains annotated genomes, evidence of transcription, proteomics evidence, protein function evidence, population biology and evolution data. Data can be queried by selecting from query grid or drop down menus. Results can be combined with each other on query history page. Search results can be downloaded with associated functional data and registered users can store their query history for future retrieval or analysis.Key community database for malaria researchers, intersecting many types of laboratory and computational data, aggregated by gene. Functional, genomic, database, malaria, parasite, data, analysis, visualization, gene, genome, annotation, transcription, proteomics, protein, evolution, FASEB list uses: SynView
is related to: GeneDB Pfalciparum
has parent organization: Eukaryotic Pathogen Database Resources
has parent organization: Pennsylvania State University
has parent organization: University of Georgia; Georgia; USA
malaria NIAID PMID:18957442 nif-0000-03314, SCR_017665 SCR_013331 PlasmoDB, Plasmodium Genomics Resource, PlasmoDB 5.5, Plasmodium genome-resource 2026-02-14 02:02:29 1239
R/FEST
 
Resource Report
Resource Website
1+ mentions
R/FEST (RRID:SCR_013347) software resource, software application An R package for simulations and likelihood calculations of pair-wise family relationships using DNA marker data. (entry from Genetic Analysis Software) gene, genetic, genomic, r is listed by: Genetic Analysis Software nlx_154111, SCR_000830, nlx_154582 SCR_013347 FEST 2026-02-14 02:02:47 2
Informatics for Integrating Biology and the Bedside
 
Resource Report
Resource Website
10+ mentions
Informatics for Integrating Biology and the Bedside (RRID:SCR_013629) i2b2 training resource, portal, data set, data or information resource, organization portal, software resource i2b2 (Informatics for Integrating Biology and the Bedside) is an NIH-funded National Center for Biomedical Computing based at Partners HealthCare System. The i2b2 Center is developing a scalable informatics framework that will enable clinical researchers to use existing clinical data for discovery research and, when combined with IRB-approved genomic data, facilitate the design of targeted therapies for individual patients with diseases having genetic origin. For some resources (e.g. software) the use of the resource requires accepting a specific (e.g. OpenSource) license. genetic, biology, biomedical, computing, genomic, health, healthcare, informatic, origin, patient, therapy, predoctoral, postdoctoral is related to: National Centers for Biomedical Computing
is parent organization of: i2b2 Cross-Institutional Clinical Translational Research project
is parent organization of: Smoking NLP Challenge Data
NLM U54LM008748 Free, Public, Acknowledgement requested nif-0000-33133 SCR_013629 2026-02-14 02:02:49 27
European large-scale functional genomics in the rat for translational research (EURATRANS)
 
Resource Report
Resource Website
European large-scale functional genomics in the rat for translational research (EURATRANS) (RRID:SCR_013697) EURATRANS data or information resource, organization portal, portal, consortium The European large-scale functional genomics in the rat for translational research (EURATRANS) consortium brings together investigators who will use next-generation sequencing technologies to generate genomic, transcriptomic and epigenomic datasets. The goal is to create quantitative metabonomic and proteomic datasets to give significant depth of coverage, at multiple levels, across pathophysiological phenotypes. The aim is to enable insights into disease mechanisms, through an integrative, cross-disciplinary approach to understanding large-scale functional genomic datasets in rats and humans. government, individual consortium, basic science, tool development, biomarker research, data-sharing enabler, genomic, transcriptomic, epigenomic, rat, European Union FP7 n HEALTH-F4-2010-241504 SCR_013697 2026-02-14 02:02:54 0
DISULFIND
 
Resource Report
Resource Website
50+ mentions
DISULFIND (RRID:SCR_016072) Disulfinder sequence analysis software, data processing software, data analysis software, software application, software resource THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023, Software for predicting the disulfide bonding state of cysteines and their disulfide connectivity, starting from a protein sequence alone and may be useful in other genomic annotation tasks. predict, disulfide, bonding, state, cysteine, protein, sequence, genomic, annotation, bio.tools is listed by: Debian
is listed by: bio.tools
is listed by: OMICtools
has parent organization: University of Florence; Florence; Italy
EU STREP APrIL II contract no. FP6-508861;
EU NoE BIOPATTERN contract no. FP6-508803;
Embark Fellowship from the Irish Research Council for Science ;
Engineering and Technology
PMID:16844986
DOI:10.1093/nar/gkl266
THIS RESOURCE IS NO LONGER IN SERVICE OMICS_04214, biotools:disulfind https://bio.tools/disulfind
https://sources.debian.org/src/disulfinder/
SCR_016072 Cysteines Disulfide Bonding State and Connectivity Predictor 2026-02-14 02:02:58 66
Cassiopee
 
Resource Report
Resource Website
Cassiopee (RRID:SCR_016056) sequence analysis software, data processing software, data analysis software, software application, software resource Software to scan an input genomic sequence (dna/rna/protein). It searchs for a subsequence that has an exact match, substitutions (Hamming distance), and/or insertion/deletions with supporting alphabet ambiguity. genomic, sequence, DNA, RNA, protein, scan, subsequence, search, match, substitution, distance, Hamming, insertion, deletion is listed by: Debian
is listed by: OMICtools
has parent organization: Durham University; Durham; England
Free, Available for download OMICS_19794 https://sources.debian.org/src/cassiopee/ SCR_016056 cassiopee-c 2026-02-14 02:03:11 0
NeMOarchive
 
Resource Report
Resource Website
100+ mentions
NeMOarchive (RRID:SCR_016152) NeMO data repository, storage service resource, data or information resource, service resource, database Data repository specifically focused on storage and dissemination of omic data generated from BRAIN Initiative and related brain research projects. Data repository and archive for BCDC and BICCN project, among others. NeMO data include genomic regions associated with brain abnormalities and disease, transcription factor binding sites and other regulatory elements, transcription activity, levels of cytosine modification, histone modification profiles and chromatin accessibility. omic, neuroscience, neurobiology, bcbc, biccn, nih, brain, genomic, region, abnormal, transcription, factor, binding, site, chromatin, regulatory, element, data is used by: BRAIN Initiative Cell Atlas Network
is used by: BICCN
is recommended by: BRAIN Initiative
is related to: NeMO Analytics
has parent organization: University of Maryland School of Medicine; Maryland; USA
NIMH MH114788;
BRAIN Initiative
Free, Freely available https://data.nemoarchive.org/ SCR_016152 NeMO Archive, Neuroscience Multi-omic Data Archive, The Neuroscience Multi-Omic Archive, Neuroscience Multi-Omic Archive 2026-02-14 02:02:59 113
Gff2aplot
 
Resource Report
Resource Website
Gff2aplot (RRID:SCR_016128) data visualization software, software resource, data processing software, software application Software application to visualize the alignment of two genomic sequences together with their annotations. Used to generate print-quality images for comparative genome sequence analysis. alignment, pair-wise, plot, genomic, sequence, visualize, together, annotate, analysis, parameter, dataset, is listed by: Debian
is listed by: OMICtools
PMID:14668236 Free, Available for download OMICS_19949 https://sources.debian.org/src/gff2aplot/ SCR_016128 2026-02-14 02:02:58 0

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