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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Heuristic Identification of Biological Architectures for simulating Complex Hierarchical Interactions Resource Report Resource Website |
Heuristic Identification of Biological Architectures for simulating Complex Hierarchical Interactions (RRID:SCR_017140) | HIBACHI, hibachi | software application, software resource, simulation software | Software tool that creates data sets with particular characteristics. Method and open source software for simulating complex biological and biomedical data to aid in comparing and evaluating machine learning methods. | data, simulation, dataset, compare, machine, evaluate, learning, method | NLM LM012601; NIAID AI116794; NIDDK DK112217 |
PMID:29218887 | Free, Available for download, Freely available | SCR_017140 | Heuristic Identification of Biological Architectures for simulating Complex Hierarchical Interactions | 2026-02-16 09:49:10 | 0 | |||||||
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SpheroScan Resource Report Resource Website 1+ mentions |
SpheroScan (RRID:SCR_023886) | data processing software, software application, software resource, image analysis software | Software tool for analyzing images of spheroids. Designed to streamline process of spheroid segmentation, area calculation, and downstream analysis of spheroid image data, and can help to standardize and accelerate analysis of spheroid assay results. | 3D spheroids, spheroids image, spheroid segmentation, spheroid image data, | Swiss National Science Foundation ; Wings for Life Spinal Cord Research Foundation ; Else Kröner-Fresenius-Stiftung ; NIDDK R01 DK077195; NIDDK R01 DK127673 |
Free, Available for download, Freely available | SCR_023886 | 2026-02-16 09:50:52 | 1 | ||||||||||
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AccuCor Resource Report Resource Website 10+ mentions |
AccuCor (RRID:SCR_023046) | data processing software, software application, software resource | Software as isotope natural abundance correction algorithm that is needed especially for high resolution mass spectrometers. Natural abundance correction of mass spectrometer data. | Natural abundance correction, mass spectrometer data, isotope natural abundance correction algorithm, high resolution mass spectrometers | NCI R01 CA163591; NIDDK P30DK019525; NCI CA211437; U. S. Department of Energy |
PMID:28471646 | Free, Available for download, Freely available | https://github.com/XiaoyangSu/AccuCor | SCR_023046 | 2026-02-16 09:50:24 | 18 | ||||||||
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Secrepedia Resource Report Resource Website |
Secrepedia (RRID:SCR_022590) | data or information resource, database, project portal, portal | Encyclopedia of white and brown adipocyte secretome in mouse models and humans as key prerequisite to elucidating role of these mediators in normal physiology and disease. | Encyclopedia, white and brown adipocyte secretome, mouse models and humans, normal physiology and disease | is listed by: NIDDK Information Network (dkNET) | type 2 diabetes, Diabetes, obesity | NIDDK | Free, Freely available | SCR_022590 | 2026-02-16 09:50:26 | 0 | ||||||||
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Childhood Liver Disease Research and Education Network Resource Report Resource Website 1+ mentions |
Childhood Liver Disease Research and Education Network (RRID:SCR_001497) | ChiLDREN | tissue bank, material resource, biomaterial supply resource | Database of clinical information and serum and tissue samples from children across the United States and Canada with Biliary Atresia, Idiopathic Neonatal Hepatitis, Cystic Fibrosis Liver Disease, Alagille Syndrome, Alpha-1 Antitrypsin Deficiency, Bile Acid Synthesis Defects, Mitochondrial Hepatopathies, and Progressive Familial Intrahepatic Cholestasis in order to facilitate research and to perform clinical, epidemiological, and therapeutic trials in these important pediatric liver diseases. Three NIDDK-funded consortia, Biliary Atresia Research Consortium (BARC), Cholestatic Liver Disease Consortium (CLiC), and the Cystic Fibrosis Liver Disease (CFLD) Network were consolidated to form ChiLDREN. Most of the ChiLDREN studies are natural history studies aimed at acquiring information and data that will provide a better understanding of these rare conditions. Participants will be asked to allow study personnel to obtain information from medical records and an interview, and to collect blood, urine, and tissue samples when clinically indicated, in order to understand the causes of these diseases and to improve the diagnosis and treatment of children with these diseases. All of the information obtained in these studies is confidential and no names or identifying information are used in the study. | child, clinical, epidemiology, therapy, pediatric, young human, rare disease, diagnostics, treatment, infant, liver, longitudinal, gall bladder, bile duct, small intestine, colon, lymph node, blood, urine, tissue, serum, plasma, dna, bile, liver tissue, gall bladder tissue, bile duct tissue, small intestine tissue, colon tissue, lymph node tissue |
is listed by: One Mind Biospecimen Bank Listing is listed by: NIDDK Information Network (dkNET) has parent organization: University of Michigan; Ann Arbor; USA |
Biliary Atresia, Idiopathic Neonatal Hepatitis, Cystic Fibrosis Liver Disease, Alagille Syndrome, Alpha-1 Antitrypsin Deficiency, Bile Acid Synthesis Defect, Mitochondrial Hepatopathy, Progressive Familial Intrahepatic Cholestasis, Liver disease, Metabolism defect, Cholestasis | NIDDK 2U01DK062456 | nlx_152755 | SCR_001497 | Childhood Liver Disease Research and Education Network (ChiLDREN) | 2026-02-16 09:45:30 | 3 | ||||||
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Assessment Serial Evaluation and Subsequent Sequelae in Acute Kidney Injury (ASSESS-AKI) Resource Report Resource Website |
Assessment Serial Evaluation and Subsequent Sequelae in Acute Kidney Injury (ASSESS-AKI) (RRID:SCR_014386) | ASSESS-AKI | data set, data or information resource, resource | A study which recruits patients with and without an episode of acute kidney injury during a hospitalization, and follows them longitudinally for major cardiac, renal and mortality events. An important aspect of the study is the prospective evaluation of potential biomarkers for renal and cardiac outcomes. | study, acute kidney injury, longitudinal, major cardiac event, major renal event, major mortality event, biomarker |
is listed by: NIDDK Research Resources is listed by: NIDDK Information Network (dkNET) |
NIDDK | Account required | http://www.niddk.nih.gov/research-funding/research-resources/Pages/default.aspx | SCR_014386 | Assessment Serial Evaluation and Subsequent Sequelae in Acute Kidney Injury | 2026-02-16 09:48:35 | 0 | ||||||
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Vitamin D to Prevent Type 2 Diabetes (D2d) Resource Report Resource Website 1+ mentions |
Vitamin D to Prevent Type 2 Diabetes (D2d) (RRID:SCR_014382) | D2d | data set, data or information resource, resource | A study to determine whether vitamin D supplementation is safe and effective in delaying the onset of type 2 diabetes in people at risk for the disease and to gain a better understanding of how vitamin D affects glucose metabolism. | diabetes, vitamin d, supplement, prevention, glucose metabolism |
is listed by: NIDDK Research Resources is listed by: NIDDK Information Network (dkNET) |
Type 2 diabetes | NIDDK | Study is ongoing | http://www.niddk.nih.gov/research-funding/research-resources/Pages/default.aspx | SCR_014382 | Vitamin D to Prevent Type 2 Diabetes | 2026-02-16 09:48:35 | 1 | |||||
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University of Pennsylvania Center for Molecular Studies in Digestive and Liver Diseases Cell Culture Core Resource Report Resource Website |
University of Pennsylvania Center for Molecular Studies in Digestive and Liver Diseases Cell Culture Core (RRID:SCR_015621) | material resource, biomaterial supply resource, cell repository | Core facility that maintains a centralized repository of cells and reagents pertinent to digestive, liver and pancreatic disease research. It also provides training for labs in new cell culture (2D and 3D) techniques. | digestive disease, liver disease, pancreatic disease, cell repository, reagent, cell culture |
is listed by: NIDDK Information Network (dkNET) has parent organization: University of Pennsylvania Center for Molecular Studies in Digestive and Liver Diseases is organization facet of: University of Pennsylvania Center for Molecular Studies in Digestive and Liver Diseases |
digestive disease, liver disease, pancreatic disease | NIDDK P30 DK050306 | Available to the research community | SCR_015621 | 2026-02-16 09:48:50 | 0 | ||||||||
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UCSF Liver Center Resource Report Resource Website 1+ mentions |
UCSF Liver Center (RRID:SCR_015595) | data or information resource, organization portal, portal | Center whose goal is to integrate bench science with clinical investigation, in support of its vision to understand and cure human liver diseases. | UCSF, liver, liver disease |
is listed by: NIDDK Information Network (dkNET) is parent organization of: UCSF Liver Center Cell Biology Core is parent organization of: UCSF Liver Center Clinical & Translational Core is parent organization of: UCSF Liver Center Immunology Core is parent organization of: UCSF Liver Center Pathology & Imaging Core has organization facet: UCSF Liver Center Cell Biology Core has organization facet: UCSF Liver Center Clinical & Translational Core has organization facet: UCSF Liver Center Immunology Core has organization facet: UCSF Liver Center Pathology & Imaging Core is organization facet of: Digestive Disease Centers |
liver disease | NIDDK P30 DK026743 | Available to the research community | SCR_015595 | 2026-02-16 09:48:50 | 2 | ||||||||
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UCSF Liver Center Cell Biology Core Resource Report Resource Website |
UCSF Liver Center Cell Biology Core (RRID:SCR_015600) | material resource, biomaterial supply resource, cell repository | Core whose purpose is providing primary and immortalized liver cells for experimental use as well as other material such as human liver cells, primary hepatocytes, and immortalized cell lines. | cell biology, cell lines, liver cells, hypatocyte |
is listed by: NIDDK Information Network (dkNET) has parent organization: UCSF Liver Center is organization facet of: UCSF Liver Center |
liver disease | NIDDK P30 DK026743 | Available to the research community | SCR_015600 | 2026-02-16 09:48:50 | 0 | ||||||||
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University of Chicago Digestive Diseases Research Core Center Integrated Translational Research Core Resource Report Resource Website |
University of Chicago Digestive Diseases Research Core Center Integrated Translational Research Core (RRID:SCR_015606) | material resource, biomaterial supply resource, cell repository | Core that serves as both a central repository for all the samples and data shared by the other cores and a catalyst for interdisciplinary research. | integrated translational research, communication, digestive disease research |
is listed by: NIDDK Information Network (dkNET) has parent organization: University of Chicago Digestive Diseases Research Core Center is organization facet of: University of Chicago Digestive Diseases Research Core Center |
digestive disease | NIDDK P30 DK042086 | Available to the research community | SCR_015606 | 2026-02-16 09:48:56 | 0 | ||||||||
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GeneRanger Resource Report Resource Website |
GeneRanger (RRID:SCR_023622) | data access protocol, software resource, web service | Web server application that provides access to processed data about expression of human genes and proteins across human cell types, tissues, and cell lines from several atlases. Used to explore single gene expression across tissues and cell types. | explore single gene expression, gene expression across tissues and cell types, gene expression, |
is related to: TargetRanger has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
NCI U24CA264250; NCI U24CA224260; NIDDK R01DK131525; NIH Office of the Director OT2OD030160; NIDDK RC2DK131995; NCI U24CA271114 |
PMID:37166966 | Free, Freely available | SCR_023622 | 2026-02-16 09:50:32 | 0 | ||||||||
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TargetRanger Resource Report Resource Website 1+ mentions |
TargetRanger (RRID:SCR_023621) | data access protocol, software resource, web service | Web server application that identifies targets from user inputted RNA-seq samples collected from cells we wish to target. By comparing inputted samples with processed RNA-seq and proteomics data from several atlases, TargetRanger identifies genes that are highly expressed in target cells while lowly expressed across normal human cell types, tissues, and cell lines. | identify targets, identify genes, user inputted RNA-seq samples, target cells, proteomics data, human cells, |
is related to: GeneRanger has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
NCI U24CA264250; NCI U24CA224260; NIDDK R01DK131525; NIH Office of the Director OT2OD030160; NIDDK RC2DK131995; NCI U24CA271114 |
PMID:37166966 | Free, Freely available | https://maayanlab.github.io/Workshop.io/generanger | SCR_023621 | 2026-02-16 09:50:49 | 2 | |||||||
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microbeMASST Resource Report Resource Website 1+ mentions |
microbeMASST (RRID:SCR_024713) | data access protocol, software resource, web service | Web taxonomically informed mass spectrometry search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging database of over 60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns. | Identification of microbial derived metabolites, microbial metabolomics data, microbial metabolite annotation, taxonomy, mass spectrometry search tool, searching tool, bacteria, fungi, metabolomics, microbiome, search known and unknown MS/MS spectra, | is related to: GNPS MASST | NIDDK U24DK133658; NIA U19AG063744; NIGMS 1DP2GM137413; Korean Government ; Austrian Science Fund ; German Research Foundation ; Sao Paulo Research Foundation ; Mexican National Council of Science and Technology ; NIGMS R01GM107550; NSF ; Research Council of Norway ; NIAID R01AI167860; NIDDK T32DK007202; NIGMS 1R01GM132649; NIGMS R35GM142938; NIDDK U01DK119702; NIH Office of the Director S10 OD021750; NLM 1R01LM013115 |
PMID:37577622 | Free, Freely available, | SCR_024713 | 2026-02-16 09:50:46 | 6 | ||||||||
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Sequencing of Idd regions in the NOD mouse genome Resource Report Resource Website 1+ mentions |
Sequencing of Idd regions in the NOD mouse genome (RRID:SCR_001483) | Sequencing of Idd regions in the NOD mouse genome | data set, data or information resource, resource | Genetic variations associated with type 1 diabetes identified by sequencing regions of the non-obese diabetic (NOD) mouse genome and comparing them with the same areas of a diabetes-resistant C57BL/6J reference mouse allowing identification of single nucleotide polymorphisms (SNPs) or other genomic variations putatively associated with diabetes in mice. Finished clones from the targeted insulin-dependent diabetes (Idd) candidate regions are displayed in the NOD clone sequence section of the website, where they can be downloaded either as individual clone sequences or larger contigs that make up the accession golden path (AGP). All sequences are publicly available via the International Nucleotide Sequence Database Collaboration. Two NOD mouse BAC libraries were constructed and the BAC ends sequenced. Clones from the DIL NOD BAC library constructed by RIKEN Genomic Sciences Centre (Japan) in conjunction with the Diabetes and Inflammation Laboratory (DIL) (University of Cambridge) from the NOD/MrkTac mouse strain are designated DIL. Clones from the CHORI-29 NOD BAC library constructed by Pieter de Jong (Children's Hospital, Oakland, California, USA) from the NOD/ShiLtJ mouse strain are designated CHORI-29. All NOD mouse BAC end-sequences have been submitted to the International Nucleotide Sequence Database Consortium (INSDC), deposited in the NCBI trace archive. They have generated a clone map from these two libraries by mapping the BAC end-sequences to the latest assembly of the C57BL/6J mouse reference genome sequence. These BAC end-sequence alignments can then be visualized in the Ensembl mouse genome browser where the alignments of both NOD BAC libraries can be accessed through the Distributed Annotation System (DAS). The Mouse Genomes Project has used the Illumina platform to sequence the entire NOD/ShiLtJ genome and this should help to position unaligned BAC end-sequences to novel non-reference regions of the NOD genome. Further information about the BAC end-sequences, such as their alignment, variation data and Ensembl gene coverage, can be obtained from the NOD mouse ftp site. | genome, sequencing, genome sequencing, insulin-dependent diabetes, c57bl/6j, single nucleotide polymorphism, genetic variation, bacterial artificial chromosome, sequence, gene, animal model, clone, annotation, contig |
lists: VEGA is listed by: NIDDK Information Network (dkNET) has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
Type 1 diabetes, Diabetes | NIAID AI 15416; NIDDK ; JDRF |
PMID:23729657 | Free, Freely available | nlx_152738 | http://www.sanger.ac.uk/resources/mouse/nod/ | SCR_001483 | Sequencing of Insulin-dependent diabetes regions in the NOD mouse genome | 2026-02-16 09:45:29 | 1 | |||
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Metscape Resource Report Resource Website 100+ mentions |
Metscape (RRID:SCR_014687) | software resource, resource, source code | A software program that allows users to visualize and interpret human metabolim and expression profiling data by providing users with a bioinformatics framework. Its features include bulding and analyzing networks of genes and compounds, identifying enriched pathways from expression profiling data, and visualizing changes in metabolite data. | metabolomics, metabolomics tool, visualization, expression profiling, gene, compound, metabolism, human |
is listed by: Metabolomics Workbench is listed by: SoftCite |
NIDDK U24 DK097153; NIDDK P30DK089503 |
PMID:22135418 | Freely available | SCR_014687 | 2026-02-16 09:48:39 | 145 | ||||||||
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Accelerating Medicines Partnership Type 2 Diabetes Knowledge Portal (AMP-T2D) Resource Report Resource Website 50+ mentions |
Accelerating Medicines Partnership Type 2 Diabetes Knowledge Portal (AMP-T2D) (RRID:SCR_003743) | AMP T2D, T2DKP | data repository, database, storage service resource, topical portal, portal, service resource, data or information resource, disease-related portal | Portal and database of DNA sequence, functional and epigenomic information, and clinical data from studies on type 2 diabetes and analytic tools to analyze these data. .Provides data and tools to promote understanding and treatment of type 2 diabetes and its complications. Used for identifying genetic biomarkers correlated to Type 2 diabetes and development of novel drugs for this disease. | type 2 diabetes, diabetes, knowledge, portal, database, repository, type II, diabetic, genetic, data, analysis, FASEB list |
is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: Consortia-pedia is listed by: NIDDK Information Network (dkNET) is related to: Accelerating Medicines Partnership - Alzheimers is related to: Accelerating Medicines Partnership - Alzheimers is related to: Accelerating Medicines Partnership Autoimmune Diseases of Rheumatoid Arthritis and Lupus is related to: Type 1 Diabetes Knowledge Portal is related to: Common Metabolic Diseases Knowledge Portal has parent organization: Foundation for the National Institutes of Health has parent organization: Accelerating Medicines Partnership |
Type 2 diabetes, Diabetes | NIH ; University of Michigan ; Broad Institute ; Fundacion Carlos Slim ; NIDDK |
Free, Freely available | SCR_014533, nlx_157976 | http://www.nih.gov/science/amp/type2diabetes.htm | SCR_003743 | , AMP Diabetes, AMP, T2D, AMP-T2D, Type 2 Diabetes Knowledge Portal, Accelerating Medicines Partnership Type 2 Diabetes, Accelerating Medicines Partnership Type 2 Diabetes Knowledge Portal, The AMP-T2D Knowledge Portal, AMP T2D, AMP Type 2 Diabetes | 2026-02-16 09:46:14 | 79 | ||||
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MOPED - Model Organism Protein Expression Database Resource Report Resource Website 1+ mentions |
MOPED - Model Organism Protein Expression Database (RRID:SCR_006065) | MOPED | data analysis service, analysis service resource, resource, database, production service resource, service resource, data or information resource | An expanding multi-omics resource that enables rapid browsing of gene and protein expression information from publicly available studies on humans and model organisms. MOPED also serves the greater research community by enabling users to visualize their own expression data, compare it with existing studies, and share it with others via private accounts. MOPED uniquely provides gene and protein level expression data, meta-analysis capabilities and quantitative data from standardized analysis utilizing SPIRE (Systematic Protein Investigative Research Environment). Data can be queried for specific genes and proteins; browsed based on organism, tissue, localization and condition; and sorted by false discovery rate and expression. MOPED links to various gene, protein, and pathway databases, including GeneCards, Entrez, UniProt, KEGG and Reactome. The current version of MOPED (MOPED 2.5) The current version of MOPED (MOPED 2.5, 2014) contains approximately 5 million total records including ~260 experiments and ~390 conditions. | protein expression, gene expression, model organism, gene, protein, pathway, proteomics, transcriptomics, data visualization, overlap plot, heatmap, dot plot, data sharing, protein localization, gene localization |
is related to: GeneCards is related to: UniProt is related to: KEGG is related to: Reactome |
Robert B McMillen Foundation ; NSF DBI0544757; NIGMS 5R01GM076680; NIDDK UO1DK072473; NIDDK 1U01DK089571 |
PMID:24350770 PMID:22139914 |
nlx_151470 | SCR_006065 | Multi-Omics Profiling Expression Database | 2026-02-16 09:46:37 | 2 | ||||||
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University of Pennsylvania Center for Molecular Studies in Digestive and Liver Diseases Resource Report Resource Website |
University of Pennsylvania Center for Molecular Studies in Digestive and Liver Diseases (RRID:SCR_015617) | UPCMSDLD | organization portal, topical portal, portal, data or information resource, disease-related portal | Center that aims to unite investigators with interests in digestive, liver and pancreatic physiology and disease in the exploration of creative experimental approaches. The scientific focus of the Center revolves around the molecular controls of cellular growth and differentiation in the digestive tract, liver and pancreas with the goal of achieving a new level of integration in biology, pathobiology, and therapy. | digestive disease, liver disease, pancreatic disease, physiology, experimental study, pathobiology, therapy |
is listed by: NIDDK Information Network (dkNET) is parent organization of: University of Pennsylvania Center for Molecular Studies in Digestive and Liver Diseases Molecular Pathology and Imaging Core is parent organization of: University of Pennsylvania Center for Molecular Studies in Digestive and Liver Diseases Host-Microbial Analytic and Repository Core is parent organization of: University of Pennsylvania Center for Molecular Studies in Digestive and Liver Diseases Genetically-Modified Mouse Core is parent organization of: University of Pennsylvania Center for Molecular Studies in Digestive and Liver Diseases Cell Culture Core has organization facet: University of Pennsylvania Center for Molecular Studies in Digestive and Liver Diseases Molecular Pathology and Imaging Core has organization facet: University of Pennsylvania Center for Molecular Studies in Digestive and Liver Diseases Host-Microbial Analytic and Repository Core has organization facet: University of Pennsylvania Center for Molecular Studies in Digestive and Liver Diseases Genetically-Modified Mouse Core has organization facet: University of Pennsylvania Center for Molecular Studies in Digestive and Liver Diseases Cell Culture Core is organization facet of: Digestive Disease Centers |
digestive disease, liver disease, pancreatic disease | NIDDK P30 DK050306 | Available to the research community | SCR_015617 | 2026-02-16 09:48:50 | 0 | |||||||
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Center for Iron and Heme Disorders at the University of Utah Resource Report Resource Website |
Center for Iron and Heme Disorders at the University of Utah (RRID:SCR_015341) | access service resource, resource, topical portal, portal, service resource, data or information resource, disease-related portal | Research center for iron and hematology research. It hosts cores that provide services for mutation generation and detection, metabolomics, and iron and heme experiments and research. In addition to these cores, it has an Enrichment Program, and Internal and External Advisory Committees, and a Pilot and Feasibility program. | iron and hematology research, mutation generation, metabolomics, enrichment progarm. |
is listed by: NIDDK Information Network (dkNET) has parent organization: University of Utah School of Medicine; Utah; USA 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 Iron and Heme Core is parent organization of: Center for Iron and Heme Disorders at the University of Utah Metabolomics Core is parent organization of: Center for Iron and Heme Disorders at the University of Utah Mutation Generation and Detection Core has organization facet: Center for Iron and Heme Disorders at the University of Utah Iron and Heme Core has organization facet: Center for Iron and Heme Disorders at the University of Utah Mutation Generation and Detection Core has organization facet: Center for Iron and Heme Disorders at the University of Utah Metabolomics Core has organization facet: Center for Iron and Heme Disorders at the University of Utah Administrative Core is organization facet of: Hematology Centers |
iron disorder, heme disorder | NIDDK U54DK110858 | Available to the research community | SCR_015341 | 2026-02-16 09:48:46 | 0 |
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