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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Trinity College Dublin; Dublin; Ireland Resource Report Resource Website 1+ mentions |
Trinity College Dublin; Dublin; Ireland (RRID:SCR_000261) | TCD | university | A public university, which is a part of the University of Dublin, and contains three main academic disciplines: Arts, Humanities and Social Sciences; Engineering, Mathematics and Sciences; and Health Sciences. The institution offers degrees at the undergraduate and graduate level. | arts, humanities, social sciences, mathematics, engineering, health sciences, Dublin, Ireland |
is related to: Pharma-Planta Consortium is related to: Biomedical Diagnostics Institute is parent organization of: ExplorEnz is parent organization of: CASBAH is parent organization of: Trinity Biobank is parent organization of: Random.org |
nlx_87233 | SCR_000261 | College of the Holy and Undivided Trinity of Queen Elizabeth near Dublin, Trinity, Trinity College Dublin, Trinity College, Trinity College Dublin - University of Dublin, University of Dublin | 2026-07-25 12:04:40 | 1 | ||||||||
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University of Florida; Florida; USA Resource Report Resource Website 1+ mentions |
University of Florida; Florida; USA (RRID:SCR_000145) | UF | university | Public research university in Gainesville, Florida, United States. Member of state university system of Florida with undergraduate and graduate programs in arts and sciences. | university, undergraduate, graduate, florida |
is listed by: Florida ExpertNet is affiliated with: Helmsley Cellular Research Hub is related to: Clinical and Translational Science Awards Consortium is related to: EnCor Biotechnology Inc. is related to: National High Magnetic Field Laboratory High B/T Core Facility is related to: National High Magnetic Field Laboratory Advanced Magnetic Resonance Imaging and Spectroscopy Core Facility is related to: Mnemiopsis Genome Project Portal is parent organization of: University of Florida College of Medicine; Florida; USA is parent organization of: ESPRIT is parent organization of: University of FLorida College of Medicine Molecular Pathology Core Facility is parent organization of: SNPper is parent organization of: ShapeComplexAtlas is parent organization of: University of Florida Labs and Facilities is parent organization of: MAPPER - Multi-genome Analysis of Positions and Patterns of Elements of Regulation is parent organization of: SobekCM is parent organization of: M-pick is parent organization of: ESPRIT-Tree is parent organization of: VIVO is parent organization of: MRM NeAt (Neurological Atlas) Mouse Brain Database is parent organization of: PASTA is parent organization of: Multi-fiber Reconstruction from DW-MRI is parent organization of: fanDTasia Java Applet: DT-MRI Processing is parent organization of: Mouse Brain Image Visualizer (MBIV) is parent organization of: Barth Syndrome Biorepository is parent organization of: Intrinsic Unscented Kalman Filter (IUKF) Tractography Software v1.0 is parent organization of: International Affective Picture System is parent organization of: FastqSifter is parent organization of: University of Florida Department of Chemistry Nuclear Magnetic Resonance Core Facility is parent organization of: University of Florida ICBR Cytometry Core Facility is parent organization of: University of Florida ICBR Bioinformatics Core Facility is parent organization of: University of Florida ICBR Electron Microscopy Core Facility is parent organization of: University of Florida ICBR Monoclonal Antibody Core Facility is parent organization of: University of Florida ICBR Gene Expression and Genotyping Core Facility is parent organization of: University of Florida ICBR NextGen DNA Sequencing Core Facility is parent organization of: University of Florida ICBR Proteomics and Mass Spectrometry Core Facility is parent organization of: Human Atlas of Neonatal Development and Early Life Immunity is parent organization of: Florida research open source synchronization tool is parent organization of: University of Florida UF Scripps Biomedical Research Bioinformatics and Statistics Core Facility is parent organization of: University of Florida Scripps Florida Histology Core Facility is parent organization of: University of Florida Health Mass Spectrometry and Proteomics Core Facility is parent organization of: University of Florida Scripps Institute for Biomedical Innovation and Technology Structural Biology Cryo Electron Microscopy Core Facility is parent organization of: University of Florida Systems Physiology and Omics Core Facility is parent organization of: University of FLorida College of Medicine Molecular Pathology Core Facility is parent organization of: University of Florida Herbert Wertheim College of Engineering Research Service Centers Core Facility is parent organization of: Herbert Wertheim University of Florida Scripps Institute for Biomedical Innovation and Technology Mouse Behavior Core Facility is parent organization of: Herbert Wertheim University of Florida Scripps Institute for Biomedical Innovation and Technology Genetic Perturbation Screening Core Facility is parent organization of: University of Florida Scripps Institute for Biomedical Innovation and Technology Flow Cytometry Core Facility is parent organization of: University of Florida Scripps Institute for Biomedical Innovation and Technology Metabolic Core Facility is parent organization of: Herbert Wertheim University of Florida Scripps Institute for Biomedical Innovation and Technology Genomics Core Facility is parent organization of: Herbert Wertheim University of Florida Scripps Institute for Biomedical Innovation and Technology Advanced Light Microscopy Core Facility is parent organization of: National MagLab University of Florida McKnight Brain Institute Advanced Magnetic Resonance Imaging and Spectroscopy AMRIS Core Facility is parent organization of: University of Florida Nanoscale Research Facility NRF Core Facility hosts: National High Magnetic Field Laboratory |
ISNI:0000 0004 1936 8091, nlx_80063, Crossref funder ID:100007698, Wikidata:Q501758, grid.15276.37 | https://ror.org/02y3ad647 | SCR_000145 | University of Florida (UF), University of Florida, UFlorida | 2026-07-25 12:04:36 | 1 | |||||||
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MS-Spectre Resource Report Resource Website 1+ mentions |
MS-Spectre (RRID:SCR_000266) | software resource | Software that provides (Quantitiave) analysis of multiple ls-ms(ms) runs, using mzXML import of raw data coming from spectrometers. | standalone software, java |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_02496 | SCR_000266 | Mass Spectrometry Analysis Software | 2026-07-25 12:04:39 | 1 | ||||||||
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GEOquery Resource Report Resource Website 10+ mentions |
GEOquery (RRID:SCR_000146) | GEOquery | software resource | Software that establishes a bridge between GEO and BioConductor. | microarray, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Expression Omnibus is related to: GEO2R has parent organization: Bioconductor has parent organization: National Institutes of Health |
PMID:17496320 | Free, Available for download, Freely available | biotools:geoquery, OMICS_01972 | https://bio.tools/geoquery, https://sources.debian.org/src/r-bioc-geoquery/ | SCR_000146 | GEOquery - Get data from NCBI Gene Expression Omnibus (GEO) | 2026-07-25 12:04:36 | 18 | |||||
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Pontifical Catholic University of Argentina School of Medical Sciences; Buenos Aires; Argentina Resource Report Resource Website |
Pontifical Catholic University of Argentina School of Medical Sciences; Buenos Aires; Argentina (RRID:SCR_000264) | School of Medical Sciences - UCA | university | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 10th,2023. Private medical school in Buenos Aires that offers degree programs in the medical sciences. Resource is in Spanish. | buenos aires, medicine, graduate, private, medical school |
has parent organization: Pontifical Catholic University of Argentina; Buenos Aires; Argentina is parent organization of: Biomedical Research Program UCA |
THIS RESOURCE IS NO LONGER IN SERVICE. | https://ror.org/0422kzb24 | http://www.uca.edu.ar/index.php/home/index/es/universidad/facultades/buenos-aires/cs-medicas | SCR_000264 | UCA School of Medical Sciences, UCA Facultad de Ciencias M�dicas, Pontificia Universidad Cat�lica Argentina Facultad de Ciencias M�dicas, Pontifical Catholic University of Argentina School of Medical Sciences | 2026-07-25 12:04:40 | 0 | ||||||
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Polish Ministry of Science and Higher Education Resource Report Resource Website 1+ mentions |
Polish Ministry of Science and Higher Education (RRID:SCR_000251) | institution | Polish governmental agency that administers governmental activities in science and higher education. Funding is provided by the state for scientific research. | funding, government, agency, higher education, scientific research, public, poland | ISNI: 0000 0001 0684 6072, Wikidata: Q4294468, grid.425823.a, Crossref funder ID: 501100004569, nlx_149369 | https://ror.org/05dwvd537 | http://www.nauka.gov.pl/en/ | SCR_000251 | Ministry of Science and Higher Education - Republic of Poland, Polish Ministry of Science Higher Education, Ministry of Science and Higher Education (Poland) | 2026-07-25 12:04:40 | 9 | ||||||||
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Polytechnic University of Catalonia; Barcelona; Spain Resource Report Resource Website 1+ mentions |
Polytechnic University of Catalonia; Barcelona; Spain (RRID:SCR_000252) | UPC | university | A public research university in Spain which specializes in the fields of architecture, engineering and technology at the undergraduate, graduate and postdoctoral level. UPC focuses heavily on internationalization, this is demonstrated through their large population of international PhD and master's degree students. They are a member of the Top Industrial Managers for Europe network and several university federations, including the Conference of European Schools for Advanced Engineering Education and Research (CESAER). | public, architecture, engineering, technology, catalan, internationalization, architecture | is parent organization of: TaxoAssignement | nlx_158613 | SCR_000252 | Universitat Politècnica de Catalunya, Universitat Politècnica de Catalunya BarcelonaTech, UPC BarcelonaTech, Universitat Politecnica de Catalunya, Universitat Politecnica de Catalunya BarcelonaTech, BarcelonaTech, Polytechnic University of Catalonia | 2026-07-25 12:04:39 | 1 | ||||||||
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Polytechnic University of Valencia; Valencia; Spain Resource Report Resource Website |
Polytechnic University of Valencia; Valencia; Spain (RRID:SCR_000255) | UPV | university | A technical university in Spain which offers degree programs in 14 different faculties, including business administration, computer science and industrial engineering at the undergraduate, graduate and postdoctoral level. The school has five different campuses. | technical, polytechnic, business administration, computer science, architecture, industrial engineering, design, cartography, fine arts, management | is parent organization of: DTI denoising | nlx_157969 | SCR_000255 | Polytechnic University of Valencia, Technical University of Valencia, Universidad Politécnica de Valencia, Universitat Politecnica de Valencia, Universitat Politècnica de València | 2026-07-25 12:04:39 | 0 | ||||||||
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Pompeu Fabra University; Barcelona; Spain Resource Report Resource Website |
Pompeu Fabra University; Barcelona; Spain (RRID:SCR_000256) | UPF | university | Public university in Spain that offers programs in social sciences and humanities, health and life sciences, international training in communication and communication sciences. Has colleges based on topics such as law, translation and interpretation, and engineering. Research is organized into economics and business, experimental sciences and health, law. | University, public, Spain, Barcelona |
is related to: EMIF is related to: Centre for Genomic Regulation; Barcelona; Spain is parent organization of: EEG time series Data Sets is parent organization of: Bern-Barcelona EEG database is parent organization of: Reliable detection of directional couplings using rank statistics is parent organization of: Characterizing unidirectional couplings between point processes and flows is parent organization of: Detecting event-related time-dependent directional couplings is parent organization of: Nonlinear time series analysis in a nutshell is parent organization of: Time-resolved and time-scale adaptive measures of spike train synchrony is parent organization of: Gene-Disease Association Type Ontology is parent organization of: DisGeNET is parent organization of: aneurIST is parent organization of: Functional Coverage of the Proteome is parent organization of: Cellular Biology of Addiction is parent organization of: GIMIAS is parent organization of: TransFIC is parent organization of: BioMoby |
Wikidata:Q24543, nlx_52215, grid.5612.0, ISNI:0000 0001 2172 2676 | https://ror.org/04n0g0b29 | SCR_000256 | Universitat Pompeu Fabra, Pompeu Fabra University, UPF Barcelona | 2026-07-25 12:04:40 | 0 | |||||||
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Sorbonne University; Paris; France Resource Report Resource Website |
Sorbonne University; Paris; France (RRID:SCR_000246) | UPMC | university | A public research university in France that emphasizes medical and scientific research centered on four themes: life and health, the living earth and environment, matter and new materials and modeling and engineering. It is a member of the Sorbonne Universities alliance. | public, engineering, modeling, environment, france, public research university, living earth |
is related to: EMIF is parent organization of: Parseq is parent organization of: Cordelier Research Center is parent organization of: XNBC |
, Wikidata: Q41497113, GRID: grid.462844.8, Crossref Funder ID: 501100019125, ISNI: 0000 0001 2308 1657, nlx_17035 | https://ror.org/02en5vm52 | SCR_000246 | , University Pierre and Marie Curie, Pierre and Marie Curie University, University Pierre et Marie Curie, Sorbonne Université; Pierre and Marie Curie University, Paris; Universite Pierre et Marie Curie | 2026-07-25 12:04:40 | 0 | |||||||
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GEArray Expression Analysis Suite 2.0 Resource Report Resource Website 1+ mentions |
GEArray Expression Analysis Suite 2.0 (RRID:SCR_000282) | software resource | THIS RESOURCE HAS BEEN DISCONTINUED, documented April 15, 2016. New GEArray Expression Analysis Suite 2.0 was released at Dec 21, 2006, please read Release Notices for details. SABiosciences' GEArray Analysis Suite uses advanced Java functionality. In order to experience full functionality of this Portal, the following free programs and upgrades for PC and Macs should be properly installed. PC Environment Downloads Browser compatibility is not an issue on Windows systems, so all operating systems running Windows 98 and above and either Internet explorer or Netscape should be fine. Java 1.4.1 or above is required--this should download automatically upon the first entry into the Portal. If this does not happen, Java 1.5 is available for download from the following URL: Java 1.5 Mac Environment Downloads Browser compatibility is an issue, and Mac Operating Systems prior to Panther are not able to fully take advantage of this Portal's functionality. These programs need to be downloaded and installed in a specific order as follows: Panther 10.3.5 (Operating System), Safari 1.2 (Compatible Internet Browser) and Java 1.4.2 (Java environment). Abstract. INTRODUCTION: Toll-like receptors (TLR) comprehend an emerging family of receptors that recognize pathogen-associated molecular patterns and promote the activation of leukocytes. Surgical trauma and ischemia-reperfusion injury are likely to provide exposure to endogenous ligands for TLR in virtually all kidney transplant recipients. METHODS: Macroarray (GEArray OHS-018.2 Series-Superarray) analyses of 128 genes involved in TLR signaling pathway were performed in nephrectomy samples of patients with chronic allograft nephropathy (CAN) and acute rejection (AR, vascular and non vascular). The analysis of each membrane was performed by GEArray Expression Analysis Suite 2.0. RESULTS: Macroarray profile identified a gene expression signature that could discriminate CAN and AR. Three genes were significantly expressed between CAN and vascular AR: Pellino 2; IL 8 and UBE2V1. In relation to vascular and non-vascular AR, there were only two genes with statistical significance: IL-6 and IRAK-3. CONCLUSION: Vascular and non-vascular AR and CAN showed different expression of a few genes in TLR pathway. The analysis of nephrectomy showed that activation of TLR pathway is present in AR and CAN. Sponsor. This work was supported by the inconditional grant from Fundao de Amparo a Pesquisa do Estado de So Paulo (FAPESP, 04/08311-6), from Conselho Nacional de Pesquisa e Desenvolvimento (CNPq) and from Fundao Osvaldo Ramos. | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30602 | SCR_000282 | GEArray | 2026-07-25 12:04:42 | 9 | ||||||||||
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BLASTPLOT Resource Report Resource Website |
BLASTPLOT (RRID:SCR_000162) | BLASTPLOT | software resource | A PERL module that can quickly plot the BLAST results from short sequences (primers, probes, reads) against reference targets. This software generates PNG graphs for all of the reference sequences associated with a BLAST result set. | perl, blast, short sequence, primer, png, png graph |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24685334 | Free, Available for download, Freely available | OMICS_01433 | SCR_000162 | 2026-07-25 12:04:37 | 0 | |||||||
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GemSIM Resource Report Resource Website |
GemSIM (RRID:SCR_000167) | GemSIM | software resource | A software package for generating realistic simulated next-generation genome sequencing reads with quality score values. The software is written in Python with a command-line user interface. | bioinformatics, simulation, sequencing, dna, rna, empirical models, Python, command-line, user interface, metagenomic, resequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge is required by: Wessim |
PMID:22336055 DOI:10.1186/1471-2164-13-74 |
Free, Available for download, Freely available | OMICS_01507, biotools:GemSIM | https://bio.tools/GemSIM | SCR_000167 | 2026-07-25 12:04:37 | 0 | ||||||
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ProteinProphet Resource Report Resource Website 10+ mentions |
ProteinProphet (RRID:SCR_000286) | software resource | Software that automatically validates protein identifications made on the basis of peptides assigned to MS/MS spectra by database search programs such as SEQUEST. | standalone software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: SourceForge |
PMID:14632076 | OMICS_02521, biotools:proteinprophet | https://bio.tools/proteinprophet | SCR_000286 | 2026-07-25 12:04:42 | 10 | ||||||||
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University of Illinois College of Pharmacy Resource Report Resource Website |
University of Illinois College of Pharmacy (RRID:SCR_000280) | university | A public pharmacy school, part of the University of Illinois. It offers a four-year professional degree program that leads to the PharmD, the highest level of professional education in pharmacy. The college also offers programs leading to six master's degrees and four doctorate degrees, covering a spectrum of research areas within the pharmaceutical sciences. | pharmacy, education, master, doctorate, pharmaceuticals, public | has parent organization: University of Illinois at Chicago; Illinois; USA | nlx_63570 | SCR_000280 | UICCP | 2026-07-25 12:04:40 | 0 | |||||||||
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University of Stuttgart; Stuttgart; Germany Resource Report Resource Website |
University of Stuttgart; Stuttgart; Germany (RRID:SCR_000153) | university | A public research university with 10 programs in disciplines of science, social science and humanities. The institution has technical programs in civil, mechanical, industrial and electrical engineering. | germany, engineering, interdisciplinary, science, social science, humanities | is parent organization of: Lipase Engineering Database | nlx_71546 | http://www.uni-stuttgart.de/index.en.html | SCR_000153 | 2026-07-25 12:04:36 | 0 | |||||||||
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iFad Resource Report Resource Website |
iFad (RRID:SCR_000271) | iFad | software resource | An R software package implementing a bayesian sparse factor model for the joint analysis of paired datasets, the gene expression and drug sensitivity profiles, measured across the same panel of samples, e.g. cell lines. | r, gene expression, drug sensitivity, analysis, drug-pathway association, gene-pathway, pathway, gene, drug |
is listed by: OMICtools has parent organization: Yale School of Medicine; Connecticut; USA |
PMID:22581178 | Free, Available for download, Freely available | OMICS_01959 | SCR_000271 | 2026-07-25 12:04:41 | 0 | |||||||
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GramCluster Resource Report Resource Website |
GramCluster (RRID:SCR_000272) | GramCluster | software resource | Software implementing a fast and accurate progressive clustering algorithm that relies on a grammar-based sequence distance and is particularly useful in clustering large datasets. | 16s sequence, cluster |
is listed by: OMICtools has parent organization: University of Nebraska; Nebraska; USA |
PMID:21167044 | Free, Available for download, Freely available | OMICS_01956 | SCR_000272 | 2026-07-25 12:04:42 | 0 | |||||||
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Postgwas Resource Report Resource Website |
Postgwas (RRID:SCR_000156) | software resource | A comprehensive software toolkit for post-processing, visualization and advanced analysis of GWAS results. | standalone software, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:23977141 | Free, Available for download, Freely available | OMICS_04393 | SCR_000156 | 2026-07-25 12:04:36 | 0 | ||||||||
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Queens University; Ontario; Canada Resource Report Resource Website |
Queens University; Ontario; Canada (RRID:SCR_000278) | university | Public university in Ontario, Canada that offers degree programs in the social sciences and engineering at both the undergraduate, graduate, postdoctorate and professional level. The university operates six research centers that focus on disciplines such as neuroscience, computing, human mobility and Southern African research. | ontario, canada, public, social science, engineering, professional degrees, undergraduate, graduate, masters, neuroscience |
is parent organization of: BLIMP: Biomedical LIterature Mining Publications is parent organization of: F-SNP: a collection of functional SNPs, specifically prioritized for disease association studies is parent organization of: Kinarm: End-Point Lab is parent organization of: Queen's University Translational Institute of Medicine TIME Core Facility |
grid.410356.5, ISNI:0000 0004 1936 8331, SCR_017061, Crossref funder ID:501100003321, Wikidata:Q1420038, nlx_63241 | https://ror.org/02y72wh86 | SCR_000278 | Queen's College at Kingston, Queens University; Kingston; Canada | 2026-07-25 12:04:41 | 0 |
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