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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Exonic Splicing Enhancer Finder Resource Report Resource Website 50+ mentions |
Exonic Splicing Enhancer Finder (RRID:SCR_002835) | data analysis service, production service resource, analysis service resource, service resource | A web-based analysis service for identifying exonic splicing enhancers in eukaryotic genes. ESEfinder accept sequences in the FASTA format. A typical mammalian gene is composed of several relatively short exons that are interrupted by much longer introns. To generate correct mature mRNAs, the exons must be identified and joined together precisely and efficiently, in a process that requires the coordinated action of five small nuclear (sn)RNAs (U1, U2, U4, U5 and U6) and more than 60 polypeptides. The inaccurate recognition of exon/intron boundaries or the failure to remove an intron generates aberrant mRNAs that are either unstable or code for defective or deleterious protein isoforms. Exonic enhancers are thought to serve as binding sites for specific serine/arginine-rich (SR) proteins, a family of structurally related and highly conserved splicing factors characterized by one or two RNA-recognition motifs (RRM) and by a distinctive C-terminal domain highly enriched in RS dipeptides (the RS domain). The RRMs mediate sequence-specific binding to the RNA, and so determine substrate specificity, whereas the RS domain appears to be involved mainly in protein-protein interactions. SR proteins bound to ESEs can promote exon definition by directly recruiting the splicing machinery through their RS domain and/or by antagonizing the action of nearby silencer elements. Sponsors: ESEfinder is supported by the Cold Spring Harbor Laboratory. | element, enhancer, eukaryotic, exon, exonic, gene, analysis, arginine, boundary, c-terminal, dipeptide, intron, isoform, mammalian, mrna, nuclear, polypeptide, protein, recognition, rna, serine, service, snrna, splice | has parent organization: Cold Spring Harbor Laboratory | Free, Freely available | nif-0000-25204 | SCR_002835 | ESEfinder | 2026-02-17 10:00:04 | 66 | ||||||||
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BiSearch: Primer Design and Search Tool Resource Report Resource Website 50+ mentions |
BiSearch: Primer Design and Search Tool (RRID:SCR_002980) | BiSearch | data analysis service, production service resource, analysis service resource, service resource | BiSearch is a primer-design algorithm for DNA sequences. It may be used for both bisulfite converted as well as for original not modified sequences. You can search various genomes with the designed primers to avoid non-specific PCR products by our fast ePCR method. This is especially recommended when primers are designed to amplify the highly redundant bisulfite treated sequences. It has the unique property of analyzing the primer pairs for mispriming sites on the bisulfite-treated genome and determines potential non-specific amplification products with a new search algorithm. The options of primer-design and analysis for mispriming sites can be used sequentially or separately, both on bisulfite-treated and untreated sequences. In silico and in vitro tests of the software suggest that new PCR strategies may increase the efficiency of the amplification. | dna, sequence, primer, design, algorithm, analysis, priming, bisulfite, genome, amplification, in vitro, in silico, amplification, epcr, cytosines | has parent organization: Hungarian Academy of Sciences; Budapest; Hungary | PXE International Inc. GVOP-3.1.1-2004-05-0143/3.0; Boolyai Janos Scholarship ; OTKA T34131; OTKA D42207 |
PMID:17022803 PMID:15653630 |
nif-0000-30170 | SCR_002980 | 2026-02-17 10:00:08 | 50 | |||||||
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Babelomics Resource Report Resource Website 100+ mentions |
Babelomics (RRID:SCR_002969) | Babelomics | data analysis service, production service resource, analysis service resource, service resource | An integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Version 4 of Babelomics integrates primary (normalization, calls, etc.) and secondary (signatures, predictors, associations, TDTs, clustering, etc.) analysis tools within an environment that allows relating genomic data and/or interpreting them by means of different functional enrichment or gene set methods. Such interpretation is made not only using functional definitions (GO, KEGG, Biocarta, etc.) but also regulatory information (from Transfac, Jaspar, etc.) and other levels of regulation such as miRNA-mediated interference, protein-protein interactions, text-mining module definitions and the possibility of producing de novo annotations through the Blast2GO system . Babelomics has been extensively re-engineered and now it includes the use of web services and Web 2.0 technology features, a new user interface with persistent sessions and a new extended database of gene identifiers. In this release GEPAS and Babelomics have integrated into a unique web application with many new features and improvements: * Data input: import and quality control for the most common microarray formats * Normalization and base calling: for the most common expression, tiling and SNP microarrays (Affymetrix and Agilent). * Transcriptomics: diverse analysis options that include well established as well as novel algorithms for normalization, gene selection, class prediction, clustering and time-series analysis. * Genotyping: stratification analysis, association, TDT. * Functional profiling: functional enrichment and gene set enrichment analysis with functional terms (GO, KEGG, Biocarta, etc.), regulatory (Transfac, Jaspar, miRNAs, etc.), text-mining, derived bioentities, protein-protein interaction analysis. * Integrative analysis: Different variables can be related to each other (e.g. gene expression to gnomic copy number) and the results subjected to functional analysis. Platform: Online tool | platform, analysis, transcriptomics, proteomics, genomics, normalization, clustering, gene, mirna, protein, interaction, text mining, genotyping, bioentity, functional profiling, statistical analysis, functional annotation, regulatory motif, microarray, fatigo, biclustering, networkminer, gepas, gene expression, FASEB list |
is listed by: OMICtools is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: BioCarta Pathways is related to: KEGG is related to: TRANSFAC is related to: JASPAR has parent organization: CIPF Bioinformatics and Genomics Department |
Spanish Ministry of Science and Innovation BIO2008-04212; Spanish Ministry of Science and Innovation CEN-2008-1002; Red Temtica de Investigacion Cooperativa en Cancer RD06/0020/1019; Instituto de Salud Carlos III |
PMID:20478823 PMID:18515841 PMID:16845052 PMID:14990455 PMID:15980512 PMID:17478504 |
Free for academic use, Account required | OMICS_00748, nif-0000-30144 | http://www.fatigo.org/ http://www.gepas.org/ http://babelomics3.bioinfo.cipf.es |
http://www.babelomics.org | SCR_002969 | Babelomics 4: Gene Expression and Functional Profiling Analysis Suite, Babelomics 4 | 2026-02-17 09:59:54 | 136 | |||
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Sanford Burnham Prebys Medical Discovery Institute Animal Imaging and Analysis Resource Report Resource Website |
Sanford Burnham Prebys Medical Discovery Institute Animal Imaging and Analysis (RRID:SCR_014851) | biomaterial supply resource, material resource | Animal imaging and analysis lab that provides imaging and analytical services for SBP investigators. The facility can perform in vivo non-invasive luminescence and fluorescence imaging for xenograft tumor growth and metastasis studies. Analytical equipment supports complete blood cell counts (CBC) and analysis of serum components revealing metabolic or organ stress from small samples of mouse blood. | animal, facility, imaging, analysis, in vivo, non invasive, luminescence imaging, fluorescence imaging, tumor, metastasis, complete blood cell count, cbc, serum, organic, mouse, blood | Commercially available | SCR_014851 | SBP Animal Imaging and Analysis, SBP Medical Discovery Institute Animal Imaging and Analysis | 2026-02-17 10:02:43 | 0 | ||||||||||
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Donald Danforth Plant Science Center Bioanalytical Chemistry Facility Resource Report Resource Website |
Donald Danforth Plant Science Center Bioanalytical Chemistry Facility (RRID:SCR_001047) | service resource, access service resource, core facility | Facility provides tools for high quality plant and biological sample analysis in proteomics, mass spectrometry, metabolomics, ionomics, and related analytical fields. It works with academic and commercial institutions and has established collaborations with many principle investigators. | Plant, sample, analysis, proteomics, mass spectrometry, metabolomics, ionomics, elemental profiling |
is listed by: ABRF CoreMarketplace has parent organization: Donald Danforth Plant Science Center |
Restricted | ABRF_194 | https://coremarketplace.org/?FacilityID=194 | http://www.scienceexchange.com/facilities/proteomics-and-mass-spectrometry-facility, https://www.danforthcenter.org/scientists-research/core-technologies/proteomics-mass-spectrometry | SCR_001047 | Danforth Center Proteomics and Mass Spectrometry Facility, Donald Danforth Plant Science Center Proteomics and Mass Spectrometry Facility, Proteomics and Mass Spectrometry Facility, Danforth Center Ionomics, Danforth Center Mass Spectrometry Facility, Danforth Center Proteomics Facility | 2026-02-17 09:59:33 | 0 | ||||||
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UAlbany Proteomics Core Facility Resource Report Resource Website |
UAlbany Proteomics Core Facility (RRID:SCR_001048) | service resource, access service resource, core facility | A core facility that provides services in the identification of individual proteins, characterization of entire protein complexes or biosimilars, and global analysis to discover changes in the proteomes of different samples. The core also specializes in the development of custom assays for quantitation of specific molecules in complex clinical samples. | proteins, biosimilars, analysis, proteomics, core facility, custom assays, quantitation |
is listed by: ScienceExchange has parent organization: University at Albany Center for Functional Genomics |
Available to the research community, Fee-for-service basis, Available to investigators at the University at Albany, Available to academic institutions, Available to commercial entities | SciEx_537 | http://www.scienceexchange.com/facilities/proteomics-core-facility-ualbany | SCR_001048 | UAlbany CFG Proteomics Core Facility, University at Albany CFG Proteomics Core Facility, University at Albany Center for Functional Genomics Proteomics Core Facility | 2026-02-17 09:59:33 | 0 | |||||||
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VectorFriends Resource Report Resource Website |
VectorFriends (RRID:SCR_001230) | VectorFriends | commercial organization, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Sequence analysis software for molecular biologists. | cloning, isothermal assembly, pcr, primer design, data management, sequence analysis, sequence, analysis, primer, windows, mac os | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02113 | SCR_001230 | 2026-02-17 09:59:35 | 0 | ||||||||
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Vanderbilt X-Ray Photoelectron Spectroscopy Lab Resource Report Resource Website |
Vanderbilt X-Ray Photoelectron Spectroscopy Lab (RRID:SCR_000897) | material resource, instrument supplier | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 13,2025.Lab with access to the PHI Versaprobe, a surface-sensitive analytical tool for identifying elemental composition and local bonding environment. | versaprobe, elemental composition, local bonding, environment, analysis, photoelectron, spectroscopy, xps |
is listed by: Eagle I has parent organization: Vanderbilt University; Tennessee; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156680 | http://eagle-i.ea.vanderbilt.edu/i/00000138-7b9d-06cc-480b-864680000000 | SCR_000897 | 2026-02-17 09:59:33 | 0 | ||||||||
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Center for Functional Neuroimaging Technologies Resource Report Resource Website 1+ mentions |
Center for Functional Neuroimaging Technologies (RRID:SCR_001423) | CFNT | biomedical technology research center, training resource, service resource, access service resource | Biomedical technology research center that develops and applies innovative neuroimaging technologies and techniques to enable closer examination of the human brain, and thereby contribute to better understanding of the brain in health and disease. They develop new techniques and advance existing technologies for acquisition and analysis of functionally specific images of the working brain, with unprecedented physiological precision and spatiotemporal resolution. The research and development aims to improve and extend existing methods for non-invasive magnetic resonance image analysis and acquisition, electromagnetic source imaging, optical neuroimaging, and most recently, combined MR-PET neuroimaging. The Resource provides an essential interactive environment, within which an interdisciplinary team of highly skilled scientists, engineers, and clinicians with diverse expertise in multiple modalities and disciplines. The resource supports service use of the Center's facilities by neuroscientists throughout the country, provide extensive training opportunities for students, fellows, and staff scientists, and seek to advance the field of brain mapping through active dissemination of new knowledge and technology. | mri, neuroimaging, pet, acquisition, analysis, brain, electromagnetic source imaging, optical neuroimaging, multimodal, magnetic resonance, eeg, meg, electrocorticography, information resource, optical imaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Harvard Medical School; Massachusetts; USA |
NIBIB 5P41EB015896-18 | Free, Available for download, Freely available | nlx_152644 | http://www.nitrc.org/projects/cfnt | SCR_001423 | 2026-02-17 09:59:37 | 1 | ||||||
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Classification of Human Lung Carcinomas by mRNA Expression Profiling Reveals Distinct Adenocarcinoma Sub-classes Resource Report Resource Website 1+ mentions |
Classification of Human Lung Carcinomas by mRNA Expression Profiling Reveals Distinct Adenocarcinoma Sub-classes (RRID:SCR_003010) | data or information resource, data set | Data set of a molecular taxonomy of lung carcinoma, the leading cause of cancer death in the United States and worldwide. Using oligonucleotide microarrays, researchers analyzed mRNA expression levels corresponding to 12,600 transcript sequences in 186 lung tumor samples, including 139 adenocarcinomas resected from the lung. Hierarchical and probabilistic clustering of expression data defined distinct sub-classes of lung adenocarcinoma. Among these were tumors with high relative expression of neuroendocrine genes and of type II pneumocyte genes, respectively. Retrospective analysis revealed a less favorable outcome for the adenocarcinomas with neuroendocrine gene expression. The diagnostic potential of expression profiling is emphasized by its ability to discriminate primary lung adenocarcinomas from metastases of extra-pulmonary origin. These results suggest that integration of expression profile data with clinical parameters could aid in diagnosis of lung cancer patients. | molecular, taxonomy, lung, carcinoma, cancer, death, mrna, expression, sequence, data, adenocarcinoma, neuroendocrine, gene, type ii pneumocyte, analysis, metastasis, integration, mrna expression profiling | has parent organization: Broad Institute | Lung cancer | NCI U01 CA84995 | PMID:11707567 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-30292 | SCR_003010 | Cancer Genomics Publication | 2026-02-17 10:00:09 | 2 | |||||
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DEAPdataset Resource Report Resource Website 10+ mentions |
DEAPdataset (RRID:SCR_001586) | DEAPdataset | data or information resource, data set | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 12,2025. Multimodal dataset for emotion analysis using EEG, Physiological and Video Signals of human affective states. The electroencephalogram (EEG) and peripheral physiological signals of 32 participants were recorded as each watched 40 one-minute long excerpts of music videos. Participants rated each video in terms of the levels of arousal, valence, like/dislike, dominance and familiarity. For 22 of the 32 participants, frontal face video was also recorded. A novel method for stimuli selection was used, utilizing retrieval by affective tags from the last.fm website, video highlight detection and an online assessment tool. The dataset is made publicly available and other researchers are encouraged to use it for testing their own affective state estimation methods. | emotion, analysis, eeg, physiological, video, signal, affective state, physiological recording, video recording | has parent organization: Queen Mary University of London; London; United Kingdom | European Community's Seventh Framework Program (FP7/2007-2011) grant agreement 216444; BrainGain Smart Mix Programme ; Swiss National Foundation for Scientific Research ; NCCR Interactive Multimodal Information Management |
THIS RESOURCE IS NO LONGER IN SERVICE. | nlx_153824 | SCR_001586 | DEAP: A Dataset for Emotion Analysis using EEG Physiological and Video Signals, DEAPDataset: A Dataset for Emotion Analysis using EEG Physiological and Video Signals | 2026-02-17 09:59:42 | 17 | ||||||
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Harvard Bioinformatics Core at Joslin Diabetes Center Resource Report Resource Website |
Harvard Bioinformatics Core at Joslin Diabetes Center (RRID:SCR_009827) | service resource, access service resource, core facility | Core for data driven projects related to basic, clinical and translational research, with a particular emphasis on diabetes. Aims to ensure that researchers take advantage of the most modern and robust methods available in the field of Bioinformatics and Biostatistics. | computational, core, data, analysis, diabetes |
is listed by: Eagle I is related to: Joslin Diabetes Center has parent organization: Harvard University; Cambridge; United States |
Diabetes | nlx_156298 | http://www.joslin.org/bioinformatics.html | SCR_009827 | The Bioinformatics and Biostatistics Core at Joslin Diabetes Center, Bioinformatics and Biostatistics Core at Joslin Diabetes Center | 2026-02-17 10:01:37 | 0 | |||||||
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Harvard School of Public Health Environmental Statistics and Bioinformatics Core Facility Resource Report Resource Website 10+ mentions |
Harvard School of Public Health Environmental Statistics and Bioinformatics Core Facility (RRID:SCR_009822) | core facility, access service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27,2023. Core provides intellectual guidance for quantitative aspects of the design and analysis of center studies and expertise in biostatistical methods, environmental risk assessment, Geographic Information System (GIS) , spatial statistics, molecular biology, bioinformatics and statistical genetics. Core runs a regular seminar series and often sponsors short courses on specialized topics of interest to the community. | core, design, analysis, guidance, biostatistical, methods, GIS, spatial, statistics, molecular, biology, genetics, seminar, course, sponsor |
is listed by: Eagle I is listed by: ScienceExchange has parent organization: Harvard T.H. Chan School of Public Health |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156290 | https://apps.sph.harvard.edu/publisher/upload/research/niehs/facility-cores/environmental-statistics-and-bioinformatics-core/index.html | SCR_009822 | Bioinformatics Core, HSPH, Environmental Statistics, Harvard School of Public Health | 2026-02-17 10:01:18 | 31 | |||||||
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Howard University Center for Computational Biology and Bioinformatics Core Facility Resource Report Resource Website |
Howard University Center for Computational Biology and Bioinformatics Core Facility (RRID:SCR_009864) | Howard CCBB, CCBB | core facility, access service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27,2023. Core for bioinformatics consultation and software access. Laboratory of Molecular Computations and Bioinformatics (LMCB) is a resource facility dedicated to the support of computational biomedical research at Howard University. Provides molecular modeling, molecular dynamics, bioinformatics, and computational quantum chemistry capabilities and support to a variety of research projects at Howard University. | data, analysis, bioinformatics, software, access, consultation, molecular, computation, biomedical, quantum, chemistry |
is listed by: Eagle I has parent organization: Howard University; Washington D.C. |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156335 | https://rcmi.howard.edu/ccbb-3/ | http://www.howard.edu/medicine/rcmi/LMCB/default.htm | SCR_009864 | , LMCB, Laboratory of Molecular Computations and Bioinformatics, Howard, CCBB | 2026-02-17 10:01:19 | 0 | |||||
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National High Magnetic Field Laboratory Ion Cyclotron Resonance Core Facility Resource Report Resource Website 1+ mentions |
National High Magnetic Field Laboratory Ion Cyclotron Resonance Core Facility (RRID:SCR_017361) | ICR, FT-ICR | service resource, access service resource, core facility | Facility provides service operations for sample analysis that requires ultrahigh resolution and high mass accuracy of Fourier Transform Ion Cyclotron Resonance. Used for research in biomolecular analysis, hydrogen-deuterium exchange and environmental and petrochemical analysis. Four FT-ICR mass spectrometers feature high magnetic fields including the world-record 21 tesla and are compatible with multiple ionization and fragmentation techniques. | FT-ICR, ICR, Ion Cyclotron Resonance, Fourier Transform Ion Cyclotron Resonance, analysis, spectrometer, magnetic, field, tesla, ionization, fragmentation, technique | is related to: Florida State University; Florida; USA | NSF ; NIH ; Department of Defense ; Department of Energy ; Florida State |
Restricted | SCR_017361 | National High Magnetic Field Laboratory Ion Cyclotron Resonance Facility, Ion Cyclotron Resonance Facility, NHMF Laboratory Cyclotron Resonance Facility | 2026-02-17 10:03:34 | 1 | |||||||
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West Virginia University Flow Cytometry and Single Cell Core Facility Resource Report Resource Website 10+ mentions |
West Virginia University Flow Cytometry and Single Cell Core Facility (RRID:SCR_017738) | service resource, access service resource, core facility | Facility provides instrumentation and scientific support for single cell analysis and sorting. Routinely performs analysis of both eukaryotic and prokaryotic cells for expression of intracellular and extracellular proteins, cell cycle, cell proliferation, cytokine production, and cell sorting based on expression of cell surface antigen(s) and/or expression of genetically engineered intercellular fluorescent proteins. | Single, cell, analysis, sorting, flow, cytometry, West Virginia, service, core | NCRR RR020866; NIGMS P30 GM103488; NIGMS P20 GM103434; NIGMS U54 GM104942; NIGMS U51 GM104942; NIH Office of the Director S10 OD016165; NIGMS P20 GM109098 |
Open | ABRF_221 | SCR_017738 | FCSCCF, WVU Flow Cytometry and Single Cell Core Facility | 2026-02-17 10:02:55 | 14 | ||||||||
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Nebraska University Medical Center Flow Cytometry Research Core Facility Resource Report Resource Website 1+ mentions |
Nebraska University Medical Center Flow Cytometry Research Core Facility (RRID:SCR_017736) | service resource, access service resource, core facility | Provides central location for flow cytometry instrumentation and education. Services include Flow Cytometry,Cell sorting, data analysis, training. Software packages to analyze data include ModFit LT, BD FACSDiva v6, Cell Quest Pro, and FlowJo vX, from facility workstations. | Flow, cytometry, cell, sorting, data, analysis, training, service, core | Nebraska Research Initiative ; Fred and Pamela Buffett Cancer Center's National Cancer Institute Cancer Support Grant ; Office of the Vice Chancellor for Research ; University of Nebraska Foundation ; Nebraska Banker Fund ; NIH NCRR Shared Instrument Program |
Open | ABRF_203 | SCR_017736 | 2026-02-17 10:03:18 | 1 | |||||||||
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EchoMRI Resource Report Resource Website 10+ mentions |
EchoMRI (RRID:SCR_017104) | material resource, instrument supplier | International research instruments company that develops, manufactures and markets NMR and CT-based whole body composition and tissue characterization equipment. | Commercial, international, research, instrument, echo, medical, system, company, NMR, CT scan, whole, body, composition, tissue, analysis | SCR_017104 | EchoMRI™ | 2026-02-17 10:03:09 | 20 | |||||||||||
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Arkansas University College of Medicine Flow Cytometry Core Facility Resource Report Resource Website |
Arkansas University College of Medicine Flow Cytometry Core Facility (RRID:SCR_017741) | service resource, access service resource, core facility | Core provides flow cytometry instrumentation and analysis. Instruments include Fortessa, FacsAria and Image Stream. | Flow, cytometry, biopolymer, proteomics, data, analysis, service, core | NIGMS P20 GM103625 | ABRF_215 | SCR_017741 | Biopolymers and Proteomics Core Facility | 2026-02-17 10:03:38 | 0 | |||||||||
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South Dakota University SD BRIN Proteomics Core Facility Resource Report Resource Website |
South Dakota University SD BRIN Proteomics Core Facility (RRID:SCR_017743) | service resource, access service resource, core facility | Core provides proteomics services to researchers from South Dakota and the surrounding region to rapidly analyze and identify protein expression patterns in their experimental systems.Develops experimental design, protocols, data analysis and interpretation.Provides consulting and advice in grant proposal, as well as data preparation to be submitted to proteomics journal according to requirements.Offers training in use of common equipment such as scanner, spot cutter, imaging software, technique and protocol issues, and sample preparation. | Proteomics, protein, expression, analysis, data, experimental, design, training, service, core | NIGMS ; Sanford School of Medicine and South Dakota Biomedical Research Infrastructure Network |
Open | ABRF_224 | SCR_017743 | Proteomics Core | 2026-02-17 10:03:38 | 0 |
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