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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SC2diseases Resource Report Resource Website 1+ mentions |
SC2diseases (RRID:SCR_019093) | analysis service resource, service resource, production service resource, database, data or information resource | Manually curated database of single cell transcriptome for human diseases. scRNA-seq database derived from numerous human studies. Provides researchers with encyclopedia of biomarkers at level of genes, cells, and diseases. | Human disease, single cell transcriptome, data, manually curated data, biomarker | National Natural Science Foundation of China | PMID:33010177 | Free, Freely available | SCR_019093 | 2026-02-12 09:47:01 | 5 | |||||||||
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Arabidopsis thaliana Protein Interactome Database Resource Report Resource Website 1+ mentions |
Arabidopsis thaliana Protein Interactome Database (RRID:SCR_001896) | AtPID | data repository, service resource, storage service resource, database, data or information resource | Centralized platform to depict and integrate the information pertaining to protein-protein interaction networks, domain architecture, ortholog information and GO annotation in the Arabidopsis thaliana proteome. The Protein-protein interaction pairs are predicted by integrating several methods with the Naive Baysian Classifier. All other related information curated is manually extracted from published literature and other resources from some expert biologists. You are welcomed to upload your PPI or subcellular localization information or report data errors. Arabidopsis proteins is annotated with information (e.g. functional annotation, subcellular localization, tissue-specific expression, phosphorylation information, SNP phenotype and mutant phenotype, etc.) and interaction qualifications (e.g. transcriptional regulation, complex assembly, functional collaboration, etc.) via further literature text mining and integration of other resources. Meanwhile, the related information is vividly displayed to users through a comprehensive and newly developed display and analytical tools. The system allows the construction of tissue-specific interaction networks with display of canonical pathways. | gene, gene expression, domain, annotation, ineractome, metabolic pathway, phylogenetic, protein, protein-protein interaction, signaling pathway, proteome, protein subcellular location, ortholog, gene regulation, pathway, phenotype |
is listed by: OMICtools is related to: Gene Ontology has parent organization: Northeast Forest University; Harbin; China |
National Basic Research Program of China 2010CB945400; National Basic Research Program of China 2007CB108800; National High Technology Research and Development Program of China 2006AA02Z313; National High Technology Research and Development Program of China 2006AA10Z129; National Natural Science Foundation of China 30870575; National Natural Science Foundation of China 30730078; Science and Technology Commission of Shanghai Municipality 06DZ22923 |
PMID:21036873 PMID:17962307 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01898, nif-0000-02585 | http://atpid.biosino.org/ | SCR_001896 | AtPID Database | 2026-02-12 09:43:15 | 8 | ||||
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Consortium for Reliability and Reproducibility Resource Report Resource Website 1+ mentions |
Consortium for Reliability and Reproducibility (RRID:SCR_003774) | CoRR | data or information resource, portal, data set | Consortium that has aggregated resting state fMRI (R-fMRI) and diffusion imaging data from laboratories around the world, creating an open science resource for the imaging community, that facilitates the assessment of test-retest reliability and reproducibility for functional and structural connectomics. Given that this was a retrospective data collection, they have focused on basic phenotypic measures that are relatively standard in the neuroimaging field, as well as fundamental for analyses and sample characterization. Their phenotypic key is organized to reflect three classifications of variables: 1) core (i.e., minimal variables required to characterize any dataset), 2) preferred (i.e., variables that were strongly suggested for inclusion due to their relative import and/or likelihood of being collected by most sites), and 3) optional (variables that are data-set specific or only shared by a few sites). CoRR includes 33 datasets consisting of: * 1629 Subjects * 3357 Anatomical Scans * 5093 Resting Functional Scans * 1302 Diffusion Scans * 300 CBF and ASL Scans | consortium, connectomics, reproducibility, resting state fmri, fmri, diffusion mri, neuroimaging, metadata standard, functional image, dti, anatomical image, functional, anatomical |
uses: Mind Research Network - COINS uses: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: 1000 Functional Connectomes Project |
NIDA ; National Natural Science Foundation of China ; Child Mind Institute ; Institute of Psychology ; Chinese Academy of Sciences ; Nathan S. Kline Institute for Psychiatric Research; New York; USA |
Registration required, (NITRC), Open unspecified license | nlx_158048 | SCR_003774 | Consortium for Reliability and Reproducibility (CoRR) | 2026-02-12 09:43:40 | 6 | ||||||
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International HapMap Project Resource Report Resource Website 5000+ mentions |
International HapMap Project (RRID:SCR_002846) | HapMap | data or information resource, database, narrative resource, experimental protocol | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A multi-country collaboration among scientists and funding agencies to develop a public resource where genetic similarities and differences in human beings are identified and catalogued. Using this information, researchers will be able to find genes that affect health, disease, and individual responses to medications and environmental factors. All of the information generated by the Project will be released into the public domain. Their goal is to compare the genetic sequences of different individuals to identify chromosomal regions where genetic variants are shared. Public and private organizations in six countries are participating in the International HapMap Project. Data generated by the Project can be downloaded with minimal constraints. HapMap project related data, software, and documentation include: bulk data on genotypes, frequencies, LD data, phasing data, allocated SNPs, recombination rates and hotspots, SNP assays, Perlegen amplicons, raw data, inferred genotypes, and mitochondrial and chrY haplogroups; Generic Genome Browser software; protocols and information on assay design, genotyping and other protocols used in the project; and documentation of samples/individuals and the XML format used in the project. | genetic variant, disease, genetic sequence, genetic variation, single nucleotide polymorphism, genetic diversity, dna, sequence, catalog, genome, chromosome, bio.tools |
is used by: BioSample Database at EBI is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: SNAP - SNP Annotation and Proxy Search is related to: Haploview is related to: NHGRI Sample Repository for Human Genetic Research is related to: DistiLD - Diseases and Traits in LD is related to: SNP at Ethnos is related to: GBrowse has parent organization: NCBI |
Chinese Academy of Sciences ; Chinese Ministry of Science and Technology ; Delores Dore Eccles Foundation ; Genome Canada ; Genome Quebec ; Hong Kong Innovation and Technology Commission ; Japanese Ministry of Education Culture Sports Science and Technology MEXT ; National Natural Science Foundation of China ; SNP Consortium ; University Grants Committee of Hong Kong ; Wellcome Trust ; W. M. Keck Foundation ; NIH |
PMID:14685227 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02940, biotools:int_hapmap_project, r3d100011835, OMICS_00273 | http://www.hapmap.org/ https://bio.tools/int_hapmap_project https://doi.org/10.17616/R3H06Q |
http://snp.cshl.org | SCR_002846 | HapMap Project | 2026-02-12 09:43:28 | 6817 | |||
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Group Information Guided ICA Resource Report Resource Website |
Group Information Guided ICA (RRID:SCR_009491) | GIG-ICA | software toolkit, software resource | Software toolbox for group-information guided Independent Component Analysis (ICA). In GIG-ICA, group information captured by standard Independent Component Analysis (ICA) on the group level is used as guidance to compute individual subject specific Independent Components (ICs) using a multi-objective optimization strategy. For computing subject specific ICs, GIG-ICA is applicable to subjects that are involved or not involved in the computation of the group information. Besides the group ICs, group information captured from other imaging modalities and meta analysis could be used as the guidance in GIG-ICA too. | computational neuroscience, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Chinese Academy of Sciences; Beijing; China |
Hundred Talent Program of the Chinese Academy of Sciences ; National Basic Research Program of China 973 Program ; National Natural Science Foundation of China 91132707; National Natural Science Foundation of China 30970770 |
PMID:23194820 | Available for download | nlx_155639 | SCR_009491 | 2026-02-12 09:44:55 | 0 | ||||||
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shinyCircoss Resource Report Resource Website 1+ mentions |
shinyCircoss (RRID:SCR_022367) | software application, software resource | Software R/Shiny application for interactive creation of Circos plot. Used for creation of Circos plot interactively. | Circos plot, interactive creation |
uses: Shiny uses: R Project for Statistical Computing is related to: RCircos is related to: RStudio is related to: CRAN |
National Key Research and Development Program of China ; National Natural Science Foundation of China ; National Program for Support of Top-notch Young Professionals ; Fundamental Research Funds for the Central Universities |
PMID:29186362 | Free, Available for download, Freely available | https://github.com/YaoLab-Bioinfo/shinyCircos | SCR_022367 | 2026-02-12 09:48:01 | 2 | |||||||
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Resting State Hemodynamic Response Function Retrieval and Deconvolution Resource Report Resource Website 1+ mentions |
Resting State Hemodynamic Response Function Retrieval and Deconvolution (RRID:SCR_023663) | rsHRF | software toolkit, software resource | Software toolbox for resting state HRF estimation and deconvolution analysis. Matlab and Python toolbox that implements HRF estimation and deconvolution from resting state BOLD signal. Used to retrieve optimal lag between events and HRF onset, as well as HRF shape. Once that HRF has been retrieved for each voxel/vertex, it can be deconvolved from time series or one can map shape parameters everywhere in brain and use it as pathophysiological indicator. Input can be 2D GIfTI, 3D or 4D NIfTI images, but also on time series matrices/vectors. Output are three HRF shape parameters for each voxel/vertex, plus deconvolved time series, and number of retrieved pseudo events. All can be written back to GIfTI or NIfTI images. | hemodynamic response function, HRF estimation and deconvolution, resting state BOLD signal, GIfTI images, NIfTI images, brain | National Natural Science Foundation of China ; Fund for Scientific Research-Flanders ; European Union Horizon 2020 Framework Programme |
PMID:34560269 | Free, Available for download, Freely available | https://github.com/compneuro-da/rsHRF | SCR_023663 | 2026-02-12 09:48:03 | 3 | |||||||
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WEGO - Web Gene Ontology Annotation Plot Resource Report Resource Website 100+ mentions |
WEGO - Web Gene Ontology Annotation Plot (RRID:SCR_005827) | WEGO | service resource, analysis service resource, production service resource, data analysis service | Web Gene Ontology Annotation Plot (WEGO) is a simple but useful tool for plotting Gene Ontology (GO) annotation results. Different from other commercial software for chart creating, WEGO is designed to deal with the directed acyclic graph (DAG) structure of GO to facilitate histogram creation of GO annotation results. WEGO has been widely used in many important biological research projects, such as the rice genome project and the silkworm genome project. It has become one of the useful tools for downstream gene annotation analysis, especially when performing comparative genomics tasks. Platform: Online tool | visualization, gene ontology, gene, annotation, comparative genomics, histogram, directed acyclic graph, genomics, genome, ontology or annotation visualization, bio.tools |
is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: BGI; Shenzhen; China |
Zhejiang University ; Chinese Academy of Sciences ; Danish Basic Research Foundation ; Ministry of Science and Technology 2002AA104250; Ministry of Science and Technology CNGI-04-15-7A; National Natural Science Foundation of China 30399120; National Natural Science Foundation of China 90208019; National Natural Science Foundation of China 30200163; National Natural Science Foundation of China 90403130 |
PMID:16845012 | Free for academic use | biotools:wego, nlx_149334 | https://bio.tools/wego | SCR_005827 | BGI WEGO - Web Gene Ontology Annotation Plotting, Web Gene Ontology Annotation Plot | 2026-02-12 09:44:18 | 386 | ||||
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HDOCK server Resource Report Resource Website 100+ mentions |
HDOCK server (RRID:SCR_024799) | software resource, web service, data access protocol | Web server for protein-protein and protein-DNA/RNA docking based on hybrid strategy. With input information for receptor and ligand molecules either amino acid sequences or Protein Data Bank structures, the server automatically predicts their interaction through hybrid algorithm of template-based and template-free docking. | Web server, protein-protein docking, protein-DNA/RNA docking, amino acid sequences, Protein Data Bank structures, receptor and ligand molecules input information, interaction prediction, | National Natural Science Foundation of China ; Huazhong University of Science and Technology ; National Key Research and Development Program of China |
PMID:28521030 PMID:32269383 |
Free, Freely available | SCR_024799 | HDOCK | 2026-02-12 09:48:05 | 304 | ||||||||
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PhaSePred Resource Report Resource Website 10+ mentions |
PhaSePred (RRID:SCR_024969) | software resource, web service, data access protocol | Web server as meta-predictor for phase-separating proteins. Displays proteome-level quantiles of different features, thus profiling PS propensity and providing crucial information for identification of candidate proteins. | meta-predictor for phase-separating proteins, proteome-level quantiles of different features, profiling PS propensity, | National Key Research and Development Program of China ; National Natural Science Foundation of China ; Clinical Medicine Plus X-Young Scholars Project of Peking University ; Fundamental Research Funds for the Central Universities |
PMID:35687670 | Free, Freely available | SCR_024969 | 2026-02-12 09:48:09 | 10 | |||||||||
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quarTeT Resource Report Resource Website 10+ mentions |
quarTeT (RRID:SCR_025258) | source code, software resource, web application | Web toolkit for studies of large scale T2T genomes. Collection of tools designed for T2T genome assembly and characterization, including reference guided genome assembly, ultra long sequence based gap filling, telomere identification, and de novo centromere prediction. Includes four modules: AssemblyMapper, GapFiller, TeloExplorer, and CentroMiner. Modules can be used alone or in combination with each other for T2T genome assembly and characterization. | Telomere-To-Telomere genomes studies, guided genome assembly, ultra long sequence based gap filling, telomere identification, de novo centromere prediction, large scale T2T genomes, assemble and analyse multiple high quality genomes, highly repetitive regions in genomes, | National Natural Science Foundation of China | PMID:37560017 | Free, Available for download, Freely available | https://github.com/aaranyue/quarTeT | SCR_025258 | quar Telomere-To-Telomere Toolkit | 2026-02-12 09:48:57 | 33 | |||||||
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NECAT Resource Report Resource Website 10+ mentions |
NECAT (RRID:SCR_025350) | source code, software resource, software application, data analysis software, data processing software | Software error correction and de-novo assembly tool for Nanopore long noisy reads. Nanopore data assembler. | Nanopore, data assembler, Nanopore long noisy reads, de-novo assembly, error correction, | National Natural Science Foundation of China ; Guangdong Basic and Applied Basic Research Foundation ; US National Institute of Food and Agriculture ; US National Science Foundation |
PMID:33397900 | Free, Available for download, Freely available | SCR_025350 | 2026-02-12 09:48:14 | 13 | |||||||||
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uAI Research Portal Resource Report Resource Website 1+ mentions |
uAI Research Portal (RRID:SCR_025870) | data or information resource, portal, software resource | AI-powered integrated research platform for one-stop analysis of medical images. Provides advanced functionality such as automatic segmentation, registration, and classification for variety of application domains. Has major merits including Advanced built-in algorithms applicable to multiple imaging modalities (i.e., CT, MR, PET, DR), diseases (i.e., tumor, neurodegenerative disease, pneumonia), and applications (i.e., diagnosis, treatment planning, follow-up); Iterative deep learning-based training strategy for fast delineation of ROIs of large-scale datasets, thereby saving clinicians' time and obtaining novel and more robust models; Modular architecture with customization and extensibility, where plugins can be designed for specific purposes. | United Imaging Intelligence Inc, medical images, clinical big data management, intelligent data annotation, 3D image rendering, radiomics analysis, deep learning model training, | National Key Research and Development Program of China ; National Natural Science Foundation of China |
PMID:37492386 | Restricted | SCR_025870 | United Imaging Intelligence uAI Research Portal | 2026-02-12 09:49:03 | 1 | ||||||||
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CB-dock2 Resource Report Resource Website 50+ mentions |
CB-dock2 (RRID:SCR_026134) | software resource, web service, data access protocol | Web server for protein-ligand blind docking, integrating cavity detection, docking and homologous template fitting. Given the three-dimensional structure of protein and ligand, can predict their binding sites and affinity for computer-aided drug discovery. | protein-ligand blind docking, integrating cavity detection, docking and homologous template fitting, predict binding sites, drug discovery, | National Natural Science Foundation of China | PMID:35609983 | Free, Freely available | SCR_026134 | 2026-02-12 09:48:31 | 55 | |||||||||
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ROGUE Resource Report Resource Website 1+ mentions |
ROGUE (RRID:SCR_026568) | source code, software resource, software application, data analysis software, data processing software | Software tool as entropy-based metric for assessing purity of single cell populations. Used to accurately quantify purity of identified cell clusters. | Assessing purity of single cell population, entropy-based metric, quantify purity, identified cell clusters, | Peking University ; National Natural Science Foundation of China |
PMID:32572028 | Free, Available for download, Freely available | SCR_026568 | 2026-02-12 09:48:41 | 1 | |||||||||
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DOSE Resource Report Resource Website 1+ mentions |
DOSE (RRID:SCR_027408) | DOSE | software toolkit, software resource | Software R package for disease ontology semantic and enrichment analysis. | disease ontology, semantic and enrichment analysis, | National Natural Science Foundation of China | PMID:25677125 | Free, Available for download, Freely available | SCR_027408 | Disease Ontology Semantic and Enrichment, Disease Ontology Semantic and Enrichment (DOSE) | 2026-02-12 09:48:52 | 8 | |||||||
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CSOmap Resource Report Resource Website 1+ mentions |
CSOmap (RRID:SCR_027636) | source code, software application, software resource | Software tool for reconstruction of cell spatial organization from single-cell RNA sequencing data based on ligand-receptor mediated self-assembly. Infers cellular spatial organization from scRNA-seq by modeling ligand–receptor-mediated self-assembly. It constructs 3D pseudo-space and quantifies cell–cell interactions for downstream visualization and hypothesis testing. | Infer cellular spatial organization from scRNA-seq, modeling ligand–receptor-mediated self-assembly, reconstruction of cell spatial organization, single-cell RNA sequencing data, construct 3D pseudo-space, quantify cell–cell interactions, | Peking University ; National Natural Science Foundation of China |
PMID:32541867 | Free, Available for download, Freely available | SCR_027636 | 2026-02-12 09:48:39 | 1 |
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