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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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C. elegans Phenotype Vocabulary Resource Report Resource Website |
C. elegans Phenotype Vocabulary (RRID:SCR_006924) | WB-PHENOTYPE | ontology, data or information resource, controlled vocabulary | A structured controlled vocabulary of Caenorhabditis elegans phenotypes. | obo |
is listed by: BioPortal has parent organization: WormBase |
nlx_157348 | SCR_006924 | 2026-08-13 09:27:39 | 0 | |||||||||
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JointSNVMix Resource Report Resource Website 10+ mentions |
JointSNVMix (RRID:SCR_006804) | JointSNVMix | data analysis software, data processing software, software resource, software application | Software that implements a probabilistic graphical model to analyze sequence data from tumor / normal pairs. The model draws statistical strength by analysing both genome jointly to more accurately classify germline and somatic mutations. It effectively reduces false positive somatic mutation predictions in tumour-normal pair sequencing data. It is highly recommended to post-process results with mutationSeq in order to filter technical artifacts. | tumor, cancer, normal, somatic mutation, mutation |
is listed by: OMICtools is related to: mutationSeq has parent organization: BC Cancer Agency |
PMID:22285562 | GNU General Public License, v3, Registration required | OMICS_00085 | SCR_006804 | 2026-08-13 09:27:41 | 10 | |||||||
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National Kidney and Urologic Diseases Information Clearinghouse Resource Report Resource Website 1+ mentions |
National Kidney and Urologic Diseases Information Clearinghouse (RRID:SCR_006842) | NKUDIC | data or information resource, narrative resource, resource, service resource, training material | Information dissemination service of the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) established to increase knowledge and understanding about diseases of the kidneys and urologic system among people with these conditions and their families, health care professionals, and the general public: online, in booklets and fact sheets, by email, and over the phone. To carry out this mission, NKUDIC works closely with a coordinating panel of representatives from Federal agencies; voluntary organizations on the national level; professional groups; and State health departments to identify and respond to informational needs about kidney and urologic diseases. NKUDIC provides the following informational products and services: * Response to inquiries about kidney and urologic diseases-ranging from information about available patient and professional education materials to statistical data. By phone (8:30 a.m. to 5 p.m. eastern time, M-F), fax, mail, and email. * Publications about specific kidney and urologic diseases, provided free of copyright, in varying reading levels. Available online or as booklets and brochures. (See our Publications Catalog.) NKUDIC also sends publications to health fairs and community events. Please contact us for more information. * Referrals to health professionals through the National Library of Medicine''''s MEDLINEplus includes a consumer-friendly listing of organizations that will assist you in your search for physicians and other health professionals. * Exhibits at professional meetings specific to kidney and urologic diseases, as well as cross-cutting professional meetings. NKUDIC exhibits at 11 professional meetings, each year, including Society of Urologic Nurses and Associates, American Urologic Association, American Society of Nephrology, National Kidney Foundation, Polycystic Kidney Disease Research Foundation, American Academy of Family Physicians, American Academy of Physician Assistants, American Nurses Association, and the National Conference for Nurse Practitioners. | statistics, publication, kidney, urologic system, bladder, renal health, renal disease |
is related to: NIDDK Information Network (dkNET) has parent organization: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is parent organization of: Urologic Diseases in America |
Kidney disease, Urologic disease | NIDDK | Free, Public | nlx_152711 | SCR_006842 | National Kidney and Urologic Diseases Information Clearinghouse (NKUDIC) | 2026-08-13 09:27:38 | 1 | |||||
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Breast Tissue Cell Lines Ontology Resource Report Resource Website |
Breast Tissue Cell Lines Ontology (RRID:SCR_006686) | MCBCC | ontology, data or information resource, controlled vocabulary | Ontology covering a comprehensive list of cell lines derived from breast tissue, both normal and pathological. The ontology in built in OWL with cross relation to classes- genetic variation, pathological condition, genes, chemicals and drugs. The relations built enable semantic query across different classes | owl | is listed by: BioPortal | nlx_157344 | SCR_006686 | 2026-08-13 09:27:35 | 0 | |||||||||
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C. elegans Gross Anatomy Vocabulary Resource Report Resource Website |
C. elegans Gross Anatomy Vocabulary (RRID:SCR_006835) | WB-BT | ontology, data or information resource, controlled vocabulary | A structured controlled vocabulary of the anatomy of Caenorhabditis elegans. | obo |
is listed by: BioPortal has parent organization: WormBase |
nlx_157347 | SCR_006835 | 2026-08-13 09:27:41 | 0 | |||||||||
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NIMH CORTEX Resource Report Resource Website 10+ mentions |
NIMH CORTEX (RRID:SCR_006837) | NIMH CORTEX | topical portal, data or information resource, data processing software, software application, software toolkit, data acquisition software, software resource, portal | A program developed by the NIMH Laboratory of Neuropsychology for data acquisition and experimental control of neurophysiological experiments. The purpose of this website is to make it easier to access new versions of NIMH CORTEX and its supporting documents. Ultimately, it is also hoped that these pages will make it easier for users to report bugs, request enhancements, and obtain help. Download the latest version and unzip it into a new sub-directory. Then read the on-line documentation. For the new user, the User''s Manuals are invaluable in specifying system requirements and giving an overview of the features and necessary hardware. The Function reference goes into more detail about how to write experiments using NIMH CORTEX. The Demos reference is a good place for new and experienced users to start to get an idea of what NIMH CORTEX can do these days. | neurophysiology, neuropsychology, behavioral control |
has parent organization: NIMH Division of Intramural Research Programs is parent organization of: MatOFF |
NIMH | nif-0000-04365 | http://www.cortex.salk.edu/ | SCR_006837 | Laboratory of Systems Neuroscience, Software and Hardware for Neurophysiology: The home of NIMH Cortex, NIMH Laboratory of Systems Neuroscience | 2026-08-13 09:27:38 | 36 | ||||||
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canSAR Resource Report Resource Website 50+ mentions |
canSAR (RRID:SCR_006794) | canSAR | data or information resource, analysis service resource, production service resource, database, service resource, data analysis service | canSAR is an integrated database that brings together biological, chemical, pharmacological (and eventually clinical) data. Its goal is to integrate this data and make it accessible to cancer research scientists from multiple disciplines, in order to help with hypothesis generation in cancer research and support translational research. This cancer research and drug discovery resource was developed to utilize the growing publicly available biological annotation, chemical screening, RNA interference screening, expression, amplification and 3D structural data. Scientists can, in a single place, rapidly identify biological annotation of a target, its structural characterization, expression levels and protein interaction data, as well as suitable cell lines for experiments, potential tool compounds and similarity to known drug targets. canSAR has, from the outset, been completely use-case driven which has dramatically influenced the design of the back-end and the functionality provided through the interfaces. The Web interface provides flexible, multipoint entry into canSAR. This allows easy access to the multidisciplinary data within, including target and compound synopses, bioactivity views and expert tools for chemogenomic, expression and protein interaction network data. | molecular target, expression, cell line, compound, molecule, protein, structure, ligand, drug, 3d, genomics, 3d complex, bioactivity, protein affinity, cell line sensitivity, pathway, annotation, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: BindingDB is related to: Gene Ontology has parent organization: Cancer Research UK |
Cancer | Cancer Research UK C309/A8274 | PMID:22013161 | CanSAR is freely available to all cancer researchers. By using canSAR you are agreeing to the Terms of Use, Https://cansar.icr.ac.uk/cansar/terms-of-use/ | biotools:cansar, nlx_149410 | https://bio.tools/cansar | SCR_006794 | 2026-08-13 09:27:34 | 56 | ||||
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Brucellosis Ontology Resource Report Resource Website |
Brucellosis Ontology (RRID:SCR_006795) | IDOBRU | ontology, data or information resource, controlled vocabulary | A biomedical ontology in the domain of zoonotic disease brucellosis that is caused by Brucella, a facultative intracellular baterium. | owl | is listed by: BioPortal | Zoonotic disease brucellosis | nlx_157345 | http://www.phidias.us/bbp/idobru/index.php | SCR_006795 | 2026-08-13 09:27:37 | 0 | |||||||
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NeuroPub Visualizer Resource Report Resource Website |
NeuroPub Visualizer (RRID:SCR_006797) | NeuroPub | data processing software, software application, data visualization software, mobile app, software resource | A NIfTI visualizer for statistical brain images (fMRI, VBM, etc) the iPad. The visualizer displays these images as overlay on the MNI standard brain. You can use it to store all your statistical images from your fMRI / VBM / TBSS studies and visualise them in 2D and 3D. Use NeuroPub as a library for your statistical images. It's the perfect app to bring to meetings, conferences, etc, and show your latest results. | magnetic resonance, fmri, vbm, tbss | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Free | nlx_155827 | http://www.nitrc.org/projects/neuropub | SCR_006797 | 2026-08-13 09:27:41 | 0 | |||||||
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REDfly Regulatory Element Database for Drosophilia Resource Report Resource Website 10+ mentions |
REDfly Regulatory Element Database for Drosophilia (RRID:SCR_006790) | REDfly | data or information resource, database, service resource, data repository, storage service resource | Curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs). Includes experimentally verified fly regulatory elements along with their DNA sequence, associated genes, and expression patterns they direct. Submission of experimentally verified cis-regulatory elements that are not included in REDfly database are welcome. | transcriptional cis-regulatory module, transcription factor binding site, dna sequence, gene, expression pattern, genome, gene expression, transcription factor, cis-regulatory module, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Drosophila anatomy and development ontologies is related to: FlyMine has parent organization: University at Buffalo; New York; USA |
NSF EF0843229; NIGMS U24 GM144232 |
PMID:20965965 PMID:18039705 PMID:16303794 |
Acknowledgement requested | OMICS_01870, biotools:redfly, nif-0000-03393 | https://bio.tools/redfly | SCR_006790 | Regulatory Element Database for Drosophilia, Regulatory Element Database | 2026-08-13 09:27:34 | 15 | ||||
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Cancer Cell Map Resource Report Resource Website 10+ mentions |
Cancer Cell Map (RRID:SCR_006792) | Cancer Cell Map | data or information resource, data access protocol, analysis service resource, production service resource, database, service resource, web service, data analysis service, software resource | It is a collection of selected human-focused cellular pathways implicated in cancer that are linked to visualization and analysis tools. Biologists can browse and search the Cancer Cell Map pathways and view gene expression data on any pathway. All data is freely available. Computational biologists can download all pathways in BioPAX format for global analysis. Software developers can build software on top of the Cancer Cell Map using the web service API. Download and install the cPath pathway database software to create a local mirror of the Cancer Cell Map. Cancer Cell Map pathways were selected based on the scientific interests of research labs at Memorial Sloan-Kettering Cancer Center. Effort was made not to duplicate information in other public pathway databases. Available pathways include: Alpha6Beta4Integrin, AndrogenReceptor, EGFR1, Hedgehog, ID, KitReceptor, NOTCH, TGFBR, TNF alpha/NF-kB, Wnt. Each pathway has around 100-400 interactions. | cancer, cell map, cellular, human cancer pathway, homo sapiens, mus musculus, rattus norvegicus | is related to: Pathway Commons | nif-0000-20919 | SCR_006792 | The Cancer Cell Map | 2026-08-13 09:27:37 | 21 | ||||||||
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Berkeley Bioinformatics Open-Source Projects Resource Report Resource Website 1+ mentions |
Berkeley Bioinformatics Open-Source Projects (RRID:SCR_006704) | BBOP | topical portal, data or information resource, software resource, portal | The BBOP, located at the Lawrence Berkeley National Labs, is a diverse group of scientific researchers and software engineers dedicated to developing tools and applying computational technologies to solve biological problems. Members of the group contribute to a number of projects, including the Gene Ontology, OBO Foundry, the Phenotypic Quality Ontology, modENCODE, and the Generic Model Organism Database Project. Our group is focused on the development, use, and integration of ontolgies into biological data analysis. Software written or maintained by BBOP is accessible through the site. | ontology, biology, computation, data analysis |
is related to: AmiGO has parent organization: Lawrence Berkeley National Laboratory is parent organization of: Blip: Biomedical Logic Programming is parent organization of: OwlSim is parent organization of: OBO is parent organization of: go-moose is parent organization of: GO Online SQL Environment (GOOSE) |
NHGRI ; NIGMS |
nlx_149171 | SCR_006704 | Berkeley BOP | 2026-08-13 09:27:33 | 1 | |||||||
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matlab-bgl Resource Report Resource Website 1+ mentions |
matlab-bgl (RRID:SCR_006981) | matlab-bgl | software toolkit, software resource, software library | A Matlab package for working with graphs that uses the Boost Graph Library to efficiently implement the graph algorithms. MatlabBGL is designed to work with large sparse graphs with hundreds of thousands of nodes. | boost graph library, matlab, c, graph | GNU General Public License, v2 | nlx_156869 | SCR_006981 | MatlabBGL - A Matlab Graph Library, MatlabBGL | 2026-08-13 09:27:37 | 3 | ||||||||
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Psort Resource Report Resource Website 100+ mentions |
Psort (RRID:SCR_007038) | PSORT | topical portal, data or information resource, data analysis software, data processing software, software application, analysis service resource, production service resource, service resource, data set, data analysis service, software resource, portal | Portal to the PSORT family of computer programs for the prediction of protein localization sites in cells, as well as other datasets and resources relevant to localization prediction. The standalone versions are available for download for larger analyses. | subcellular, localization, prediction, gram, gram-positive, gram-negative, sequence, fasta, protein, protein localization, cell, motif, profile, amino acid, subcellular localization |
is listed by: OMICtools is related to: PSORT II has parent organization: Simon Fraser University; British Columbia; Canada |
OMICS_01634, nif-0000-31883 | http://psort.hgc.jp/ | SCR_007038 | Psort.org, PSORT: Prediction of Protein Sorting Signals and Localization Sites in Amino Acid Sequences | 2026-08-13 09:27:42 | 222 | |||||||
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Association for the Scientific Study of Consciousness Resource Report Resource Website 1+ mentions |
Association for the Scientific Study of Consciousness (RRID:SCR_007154) | ASSC | topical portal, data or information resource, community building portal, portal |
An academic society that promotes rigorous research directed toward understanding the nature, function, and underlying mechanisms of consciousness. The ASSC includes members working in the fields of cognitive science, medicine, neuroscience, philosophy, and other relevant disciplines in the sciences and humanities. The ASSC web site has several main functions: * coordinating annual conferences on aspects of the scientific study of consciousness. * promotion of other activities in the field (smaller conferences, mailing lists, bibliographic resource, etc). * facilitate consciousness research with awards for new investigators. * publication of papers relevant to the scientific study of consciousness in the inter-disciplinary journal Psyche. The ASSC Students community''s aim is to foster greater involvement of graduate students within the Association for the Scientific Study of Consciousness (ASSC) and improve ways in which the ASSC serves the needs of its student members. Its primary goal is to promote research and debate about consciousness among new researchers. It organizes activities like the current essay contest, details of which are on the news page. It also manage the student pages of the ASSC website and conduct occasional surveys of the ASSC student members. |
cognitive, consciousness, humanities, medicine, neuroscience, philosophy, cognitive science | nif-0000-10156 | http://assc.caltech.edu/index.htm | SCR_007154 | 2026-08-13 09:27:39 | 3 | |||||||||
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Automatic Primer Design Resource Report Resource Website 1+ mentions |
Automatic Primer Design (RRID:SCR_007155) | data processing software, software application, production service resource, service resource, data acquisition software, software resource | This automatic primer design service uses the Primer3 Software (through EMBOSS primer3 interface) to design two sets of primers for doing a nested PCR. The input can either be in Fasta format or in GENOTRACE output format. You will have to indicate with square brackets which region should be included in the amplicon. Primers for multiple amplicons (for example all exons) can be designed in a single run. | primer, design, service, software, pcr | has parent organization: Royal Netherlands Academy of Arts and Sciences; Amsterdam; Netherlands | nif-0000-30136 | SCR_007155 | Primer Design Form | 2026-08-13 09:27:44 | 1 | |||||||||
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Parkinsons UK Brain Bank Resource Report Resource Website 1+ mentions |
Parkinsons UK Brain Bank (RRID:SCR_007030) | UKPDSTB | material resource, brain bank, tissue bank, biomaterial supply resource | A brain bank of the United Kingdom which collects human brains for Parkinsons disease research. The collection is comprised of brain, spinal cord and a sample of cerebrospinal fluid from people with and without Parkinson's after death. Researchers can fill out a brain tissue request form to order samples from the bank. | tissue, brain, spinal cord, parkinson's disease, normal control, brain tissue, cerebral spinal fluid, snap frozen, fixed, frozen, cryopreserved, clinical data, post-mortem |
is listed by: One Mind Biospecimen Bank Listing has parent organization: Imperial College London; London; United Kingdom has parent organization: Parkinsons UK |
Parkinson's disease, Normal control | Parkinson's Disease Society of the United Kingdom ; Imperial College London; London; United Kingdom |
Free, Available to the research community, Charged only for tissue preparation and transport | SCR_005244, nlx_144249, nlx_35543 | http://www.parkinsonstissuebank.org.uk/index.htm | SCR_007030 | Parkinson's UK Brain Bank, UK Parkinson's Disease Society Tissue Bank, UK PDS Tissue Bank, UK Parkinson's Disease Society Tissue Bank at Imperial College London | 2026-08-13 09:27:42 | 2 | ||||
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Mouse Genome Databases Resource Report Resource Website 1+ mentions |
Mouse Genome Databases (RRID:SCR_007147) | MGD | topical portal, data or information resource, organism-related portal, database, data set, portal | A mouse-related portal of genomic databases and tables of mouse brain data. Most files are intended for you to download and use on your own personal computer. Most files are available in generic text format or as FileMaker Pro databases. The server provides data extracted and compiled from: The 2000-2001 Mouse Chromosome Committee Reports, Release 15 of the MIT microsatellite map (Oct 1997), The recombinant inbred strain database of R.W. Elliott (1997) and R. W. Williams (2001), and the Map Manager and text format chromosome maps (Apr 2001). * LXS genotype (Excel file): Updated, revised positions for 330 markers genotyped using a panel of 77 LXS strain. * MIT SNP DATABASE ONLINE: Search and sort the MIT Single Nucleotide Polymorphism (SNP) database ONLINE. These data from the MIT-Whitehead SNP release of December 1999. * INTEGRATED MIT-ROCHE SNP DATABASE in EXCEL and TEXT FORMATS (1-3 MB): Original MIT SNPs merged with the new Roche SNPs. The Excel file has been formatted to illustrate SNP haplotypes and genetic contrasts. Both files are intended for statistical analyses of SNPs and can be used to test a method outlined in a paper by Andrew Grupe, Gary Peltz, and colleagues (Science 291: 1915-1918, 2001). The Excel file includes many useful equations and formatting that will help in navigating through this large database and in testing the in silico mapping method. * Use of inbred strains for the study of individual differences in pain related phenotypes in the mouse: Elissa J. Chesler''s 2002 dissertation, discussing issues relevant to the integration of genomic and phenomic data from standard inbred strains including genetic interactions with laboratory environmental conditions and the use of various in silico inbred strain haplotype based mapping algorithms for QTL analysis. * SNP QTL MAPPER in EXCEL format (572 KB, updated January 2002 by Elissa Chesler): This Excel workbook implements the Grupe et al. mapping method and outputs correlation plots. The main spreadsheet allows you to enter your own strain data and compares them to haplotypes. Be very cautious and skeptical when using this spreadsheet and the technique. Read all of the caveates. This excel version of the method was developed by Elissa Chesler. This updated version (Jan 2002) handles missing data. * MIT SNP Database (tab-delimited text format): This file is suitable for manipulation in statistics and spreadsheet programs (752 KB, Updated June 27, 2001). Data have been formatted in a way that allows rapid acquisition of the new data from the Roche Bioscience SNP database. * MIT SNP Database (FileMaker 5 Version): This is a reformatted version of the MIT Single Nucleotide Polymorphism (SNP) database in FileMaker 5 format. You will need a copy of this application to open the file (Mac and Windows; 992 KB. Updated July 13, 2001 by RW). * Gene Mapping and Map Manager Data Sets: Genetic maps of mouse chromosomes. Now includes a 10th generation advanced intercross consisting of 500 animals genetoyped at 340 markers. Lots of older files on recombinant inbred strains. * The Portable Dictionary of the Mouse Genome, 21,039 loci, 17,912,832 bytes. Includes all 1997-98 Chromosome Committee Reports and MIT Release 15. * FullDict.FMP.sit: The Portable Dictionary of the Mouse Genome. This large FileMaker Pro 3.0/4.0 database has been compressed with StuffIt. The Dictionary of the Mouse Genome contains data from the 1997-98 chromosome committee reports and MIT Whitehead SSLP databases (Release 15). The Dictionary contains information for 21,039 loci. File size = 4846 KB. Updated March 19, 1998. * MIT Microsatellite Database ONLINE: A database of MIT microsatellite loci in the mouse. Use this FileMaker Pro database with OurPrimersDB. MITDB is a subset of the Portable Dictionary of the Mouse Genome. ONLINE. Updated July 12, 2001. * MIT Microsatellite Database: A database of MIT microsatellite loci in the mouse. Use this FileMaker Pro database with OurPrimersDB. MITDB is a subset of the Portable Dictionary of the Mouse Genome. File size = 3.0 MB. Updated March 19, 1998. * OurPrimersDB: A small database of primers. Download this database if you are using numerous MIT primers to map genes in mice. This database should be used in combination with the MITDB as one part of a relational database. File size = 149 KB. Updated March 19, 1998. * Empty copy (clone) of the Portable Dictionary in FileMaker Pro 3.0 format. Download this file and import individual chromosome text files from the table into the database. File size = 231 KB. Updated March 19, 1998. * Chromosome Text Files from the Dictionary: The table lists data on gene loci for individual chromosomes. | gene, genetic, chromosome, genotype, inbred mouse strain, pain, phenotype, polygenic, recombinant, trait, genome, genomic, single nucleotide polymorphism, primer, brain, recombinant inbred mouse strain |
has parent organization: University of Tennessee Health Science Center; Tennessee; USA is organization facet of: Alliance of Genome Resources |
nif-0000-20982 | SCR_007147 | 2026-08-13 09:27:44 | 2 | |||||||||
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Cellular Imaging and Analysis Resource Report Resource Website 10+ mentions |
Cellular Imaging and Analysis (RRID:SCR_007149) | topical portal, data or information resource, portal | PerkinElmer designs, manufactures and delivers advanced technology solutions that address the world''s most critical health and safety concerns, including maternal and fetal health, clean water and air, and safe food and toys. It''s expertise combines science, innovation and a culture of operational excellence to offer our customers technology services and support that improve the quality of people''s lives worldwide. | manufacture, deliver, technology, solution, health, safety, material, fetal, clean, water, air, food, toy, science, innovation, culture | nif-0000-30319 | SCR_007149 | 2026-08-13 09:27:39 | 37 | |||||||||||
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Lyngby Resource Report Resource Website 1+ mentions |
Lyngby (RRID:SCR_007143) | Lyngby | data analysis software, data processing software, software resource, software application | Matlab toolbox for the analysis of functional neuroimages (PET, fMRI). The toolbox contains a number of models: FIR-filter, Lange-Zeger, K-means clustering among others, visualizations and reading of neuroimaging files. | functional, statistical, fmri, pet, matlab, neuroimaging |
is listed by: Biositemaps has parent organization: THOR Center for Neuroinformatics |
Human Brain Project ; Danish Research Council ; European Union ; BIOMED2 ; MAPAWAMO ; NASA ; NSF ; DOE ; NIDA R01 DA09246; NIMH P20 MH57180 |
Free, Non-commercial | nif-0000-00324 | SCR_007143 | Lyngby Toolbox, Lyngby - A Toolbox for Functional Neuroimaging | 2026-08-13 09:27:44 | 2 |
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