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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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flowPeaks Resource Report Resource Website |
flowPeaks (RRID:SCR_000407) | software resource | Software for fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means. | software package, mac os x, unix/linux, windows, r, clustering, flow cytometry, gating, bio.tools |
is listed by: OMICtools is listed by: GitHub is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:22595209 | Free, Available for download, Freely available | biotools:flowpeaks, OMICS_05604 | http://www.bioconductor.org/packages/devel/bioc/html/flowPeaks.html, https://bio.tools/flowpeaks | SCR_000407 | 2026-08-01 12:01:20 | 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 | 2026-08-01 12:01:16 | 9 | ||||||||||
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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 | 2026-08-01 12:01:10 | 10 | ||||||||
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MiRdup Resource Report Resource Website 1+ mentions |
MiRdup (RRID:SCR_000316) | software resource | A software used for the validation of pre-miRNAs predictions as well as predict the final structure of mature miRNA. | pre-miRNA, miRNA, mRNA, splicing, predictions |
is listed by: OMICtools has parent organization: McGill University; Montreal; Canada |
PMID:23748953 | Free, Available for download, Freely available | OMICS_00404 | https://www.cs.mcgill.ca/~blanchem/mirdup/ | http://This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or any later version. | SCR_000316 | 2026-08-01 12:01:11 | 1 | ||||||
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QUALIFIER Resource Report Resource Website |
QUALIFIER (RRID:SCR_000389) | software resource | Software that provides quality control and quality assessment tools for gated flow cytometry data. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, infrastructure |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23020243 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05618 | SCR_000389 | QUALIFIER - Quality Control of Gated Flow Cytometry Experiments | 2026-08-01 12:01:16 | 0 | |||||||
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Scribe Resource Report Resource Website |
Scribe (RRID:SCR_000423) | Scribe | software resource | Scribe encodes papers to populate the BrainMap Database | magnetic resonance, pet, spect |
is used by: brainmap.org is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) |
Free, Freely available | nlx_155958 | SCR_000423 | 2026-08-01 12:01:20 | 0 | ||||||||
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GraphPad Resource Report Resource Website 1000+ mentions |
GraphPad (RRID:SCR_000306) | commercial organization | A commercial graphing software company that offers scientific software for statistical analyses, curve fitting and data analysis. It offers four programs: Prism, InStat, StatMate and QuickCalcs. | company, data, graph, scientific, statistical, analysis, curve, fitting |
is listed by: SoftCite is parent organization of: GraphPad Prism |
Restricted | nlx_156835 | SCR_000306 | 2026-08-01 12:01:14 | 1284 | |||||||||
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Altmetric Bookmarklet Resource Report Resource Website |
Altmetric Bookmarklet (RRID:SCR_000427) | Altmetric Bookmarklet | software resource | Free bookmarklet for Chrome, Firefox and Safari that allows you to instantly get article level metrics for any recent paper. Simply drag the button below to your bookmarks bar, navigate to a journal article page, and hit Altmetric it! | altmetrics, chrome, firefox, safari | is listed by: FORCE11 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156030 | http://www.force11.org/node/4720 | SCR_000427 | The Altmetric Bookmarklet | 2026-08-01 12:01:13 | 0 | ||||||
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Washington University in St. Louis; Missouri; USA Resource Report Resource Website 1+ mentions |
Washington University in St. Louis; Missouri; USA (RRID:SCR_000343) | WUSTL, WashU | university | Private research university in Greater St. Louis with its main campus mostly in unincorporated St. Louis County, Missouri and Clayton, Missouri. | missouri, undergraduate, postgraduate, graduate, university |
uses: Scizzle uses: Research Accelerator is affiliated with: Diabetes Research Centers is related to: Alzheimers Disease Genetics Consortium is related to: Clinical and Translational Science Awards Consortium is related to: Urinary Stone Disease Research Network is related to: Connectome Workbench is parent organization of: Washington University School of Medicine Knight Alzheimers Disease Research Center is parent organization of: DicomBrowser is parent organization of: Washington University School of Medicine Genome Technology Access Center Core Facility is parent organization of: DiMO is parent organization of: Washington University Neuromuscular Disease Center is parent organization of: Surface-Based Atlases is parent organization of: Neurologic AIDS Research Consortium is parent organization of: SomaticSniper is parent organization of: SPLINTER is parent organization of: DGIdb is parent organization of: Bayesian Analysis of Common NMR Problems is parent organization of: Genome Center BLAST Server is parent organization of: Washington University in St. Louis Neuroscience is parent organization of: Nematode.net is parent organization of: Human Gut Microbiome Initiative is parent organization of: Adaptive Poisson-Boltzmann Solver is parent organization of: Human Connectome Coordination Facility is parent organization of: MuSiC is parent organization of: Washington University School of Medicine in St. Louis; Missouri; USA is parent organization of: WUSTL Hybridoma Center is parent organization of: WUSTL Mouse Cardiovascular Phenotyping Core is parent organization of: WUSTL NNIN - Nano Research Facility is parent organization of: WUSTL Biology Department Imaging Facility is parent organization of: WUSTL Histology Core is parent organization of: Washington University in St. Louis School of Medicine Division of Biology and Biomedical Sciences is parent organization of: Collaborative Study on the Genetics of Alcoholism is parent organization of: Stroke Trials Registry is parent organization of: Neurology Image Library from The Internet Stroke Center is parent organization of: WormBase is parent organization of: ConnectomeDB is parent organization of: NIMH Repository and Genomics Resources is parent organization of: GLMdenoise: a fast, automated technique for denoising task-based fMRI data is parent organization of: Washington University Center for Diabetes Translation Research Administrative Core in Diabetes Research Core is parent organization of: Washington University Center for Diabetes Translation Research Dissemination and Implementation in Diabetes Research Core Facility is parent organization of: Washington University Center for Diabetes Translation Research Solutions to Diabetes in Black Americans Core is parent organization of: Washington University Center for Diabetes Translation Research Health Informatics in Diabetes Research Core is parent organization of: Washington University Center for Diabetes Translation Research is parent organization of: Washington University Center for Diabetes Translation Research Policy and Systems Science Analysis in Diabetes Research Core is parent organization of: Washington University Center for Diabetes Translation Research Health Communication and Health Literacy Core Facility is parent organization of: Washington University Center for Diabetes Translation Research Research Partnerships with American Indian/Alaskan Native Communities Core is parent organization of: Washington University School of Medicine Genome Technology Access Center Core Facility is parent organization of: Rodent Arena Tracker project is parent organization of: SnackClock is parent organization of: Feeding Experimentation Device project is parent organization of: Washington University in St. Louis Human Cells, Tissues, and Organoids Core Facility is parent organization of: Washington University School of Medicine Mass Spectrometry Technology Access Center Core Facility is parent organization of: Washington University in St. Louis Washington University Center for Cellular Imaging Core Facility is parent organization of: Washington University Digestive Diseases Research Core Center Biobank Core is parent organization of: Washington University School of Medicine Diabetes Research Center Translational Diagnostics Core is parent organization of: Washington University School of Medicine Diabetes Research Center Cell and Tissue Imaging Core is parent organization of: Washington University School of Medicine Diabetes Research Center Mass Spectrometry Core has organization facet: VarScan |
SCR_017964, Wikidata:Q777403, Crossref funder ID:100007268, ISNI:0000 0001 2355 7002, grid.4367.6, nlx_47548 | https://ror.org/01yc7t268 | SCR_000343 | Washington University | 2026-08-01 12:01:17 | 1 | |||||||
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University of Zaragoza; Zaragoza; Spain Resource Report Resource Website |
University of Zaragoza; Zaragoza; Spain (RRID:SCR_000341) | UZ | university | An undergraduate and postgraduate university which is located in Zaragoza, Spain. | zaragoza, university, undergraduate, postgraduate | is parent organization of: BCIZaragoza - YouTube | nlx_144537 | SCR_000341 | University of Zaragoza, Universidad de Zaragoza | 2026-08-01 12:01:14 | 0 | ||||||||
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University of Zurich; Zurich; Switzerland Resource Report Resource Website 1+ mentions |
University of Zurich; Zurich; Switzerland (RRID:SCR_000342) | UZH | university | University located in Zürich, Switzerland was founded in 1833. Has faculties in Philosophy, Human Medicine, Economic Sciences, Law, Mathematics and Natural Sciences, Theology and Veterinary Medicine. Offers the widest range of subjects and courses of any Swiss higher education institution. As of October 2018, 23 Nobel laureates and 1 Turing Award winner have been affiliated with University of Zurich as alumni, faculty or researchers. | immunology, genetics, neuroscience, structural biology, medicine, master, bachelor, phd |
is parent organization of: Connectome Wiki is parent organization of: Swiss Institute of Allergy and Asthma Research is parent organization of: MLTreeMap is parent organization of: University of Zurich SCRM - Cell-and Tissue Biobank is parent organization of: HPC-CLUST is parent organization of: Segmented ssTEM stack of neural tissue is parent organization of: Low Resolution Electromagnetic Tomography is parent organization of: Institute of Neuroinformatics is parent organization of: Institute for Neuroinformatics: Cortex 3D is parent organization of: TrakEM2 is parent organization of: B-Fabric is parent organization of: MINAS - Metal Ions in Nucleic AcidS is parent organization of: sLORETA is parent organization of: exact Low Resolution Electromagnetic Tomography is parent organization of: Grid Enabled Molecular Science Through Online Networked Environments is parent organization of: CATALYSTLite is parent organization of: imctools is parent organization of: Hierarchical Unsupervised Generative Embedding toolbox is parent organization of: PAXdb is parent organization of: University of Zurich Center for Microscopy and Image Analysis Core Facility is parent organization of: Progenetix |
nlx_15354 | SCR_000342 | University of Zurich, Universitat Zurich | 2026-08-01 12:01:11 | 1 | ||||||||
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University of Utah School of Medicine; Utah; USA Resource Report Resource Website |
University of Utah School of Medicine; Utah; USA (RRID:SCR_000339) | university | An university in Utah which provides opportunities in teaching, research and clinical experience for developing physicians. This organization provides MD degrees, physician training, residency, fellowship specialty training and degrees in public health or research. | university, clinic, physician training, residency, fellowship specialty training, md, public health, research |
is related to: Collaboratory of AIDS Researchers for Eradciation (CARE) has parent organization: University of Utah; Utah; USA is parent organization of: HyperBrain is parent organization of: Phevor is parent organization of: Webvision - The Organization of the Retina and Visual System is parent organization of: FURTHeR is parent organization of: Center for Iron and Heme Disorders at the University of Utah is parent organization of: Center for Iron and Heme Disorders at the University of Utah Mutation Generation and Detection Core is parent organization of: Center for Iron and Heme Disorders at the University of Utah Administrative Core is parent organization of: Center for Iron and Heme Disorders at the University of Utah Metabolomics Core |
nlx_99359 | SCR_000339 | 2026-08-01 12:01:11 | 0 | ||||||||||
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fqzcomp Resource Report Resource Website 1+ mentions |
fqzcomp (RRID:SCR_000299) | fqzcomp | software resource | A basic fastq compressor, designed primarily for high performance. | c++ |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23533605 | Free, Available for download, Freely available | OMICS_00957 | SCR_000299 | 2026-08-01 12:01:13 | 1 | |||||||
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Defense Advanced Research Projects Agency Resource Report Resource Website 1+ mentions |
Defense Advanced Research Projects Agency (RRID:SCR_000330) | DARPA | nonprofit organization | A military affiliated research institute which focuses on funding and approving new and ongoing programs while ensuring a balanced investment portfolio. This organization is mainly concerned with making investments in technologies that can be used for national security. | national security, technology, grant. investment portfolio, investments, funding, government granting agency | has parent organization: U.S. Department of Defense | Crossref funder ID: 100000185, nlx_152039, grid.421816.8, ISNI: 0000 0000 9580 5207, Wikidata: Q207361 | https://ror.org/02caytj08 | SCR_000330 | 2026-08-01 12:01:14 | 9 | ||||||||
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Indeed Resource Report Resource Website 1+ mentions |
Indeed (RRID:SCR_000292) | Indeed | job resource | A database of job listings | employment, career |
is used by: NIF Data Federation is related to: Integrated Jobs |
nlx_144165 | SCR_000292 | Indeed.com, indeed: one search. all jobs | 2026-08-01 12:01:13 | 2 | ||||||||
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Gene Bridges Resource Report Resource Website 1+ mentions |
Gene Bridges (RRID:SCR_000483) | Gene Bridges | commercial organization | A biotech company that commercializes its patented Red/ET recombination worldwide as licenses and supplies several products for the pharmaceutical and biotech industry as well as academia. It operates from the Technologie Park in Heidelberg and provides customized in-house DNA modification of any kind. Recombineering with Red/ET allows cloning, subcloning and modification of DNA at any chosen position. It permits precise engineering of DNA molecules of any size, including very large ones such as BACs or the E.coli chromosome. | recombineering, red/et recombination, license, dna modification, dna, recombination kit | is related to: AgedBrainSYSBIO | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_158134 | SCR_000483 | Gene Bridges - The Recombineering Company, Gene Bridges GmbH | 2026-08-01 12:01:19 | 3 | |||||||
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miRprimer Resource Report Resource Website 1+ mentions |
miRprimer (RRID:SCR_000480) | miRprimer | software resource | Software tool for automatic design of primers for PCR amplification of microRNAs using the method miR-specific RT-qPCR (Balcells, I., Cirera, S., and Busk, P.K. (2011). Specific and sensitive quantitative RT-PCR of miRNAs with DNA primers. BMC Biotechnol. 11, 70). | ruby, primer, microrna, rt-qpcr, ms windows, pcr amplification |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24472427 | Free, Available for download, Freely available | OMICS_02311 | SCR_000480 | miRprimer - Automatic design of primers for miR-specific RT-qPCR | 2026-08-01 12:01:18 | 3 | ||||||
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ARB project Resource Report Resource Website 10+ mentions |
ARB project (RRID:SCR_000515) | ARB | software resource | Software environment for maintaining databases of molecular sequences and additional information, and for analyzing the sequence data, with emphasis on phylogeny reconstruction. Programs have primarily been developed for ribosomal ribonucleic acid (rRNA) sequences and, therefore, contain special tools for alignment and analysis of these structures. However, other molecular sequence data can also be handled. Protein gene sequences and predicted protein primary structures as well as protein secondary structures can be stored in the same database. ARB package is designed for graphical user interface. Program control and data display are available in a hierarchical set of windows and subwindows. Majority of operations can be controlled using mouse for moving pointer and the left mouse button for initiating and performing operations. | rrna sequence, rrna, phylogeny, alignment, analysis, protein, gene |
is listed by: Debian is related to: SILVA is related to: SINA has parent organization: Technical University of Munich; Bavaria; Germany |
PMID:14985472 | Free, Available for download, Freely available | OMICS_01515 | https://sources.debian.org/src/arb/ | SCR_000515 | The ARB project | 2026-08-01 12:01:23 | 28 | |||||
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pyQPCR Resource Report Resource Website |
pyQPCR (RRID:SCR_000471) | pyQPCR | software resource | A GUI application written in python that deals with quantitative PCR (QPCR) raw data. Using quantification cycle values extracted from QPCR instruments, it uses a proven and universally applicable model to give finalized quantification resu | quantitative pcr, python, qt |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_02326 | SCR_000471 | 2026-08-01 12:01:14 | 0 | ||||||||
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PGS Resource Report Resource Website |
PGS (RRID:SCR_000475) | software resource | Software tool for association study of high-dimensional microRNA expression data with repeated measures. The penalized regression model incorporates a grid search method for analyzing associations of high-dimensional microRNA expression data with repeated measures. | standalone software, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:24947752 | Free, Available for download, Freely available | biotools:pgs, OMICS_04651 | https://bio.tools/pgs | SCR_000475 | PGS: Penalized GEE with Grid Search, Penalized GEE with Grid Search | 2026-08-01 12:01:22 | 0 |
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