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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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netClass Resource Report Resource Website |
netClass (RRID:SCR_005672) | netClass | software resource | An R package for network-based feature (gene) selection for biomarkers discovery via integrating biological information. The package adapts the following 5 algorithms for classifying and predicting gene expression data using prior knowledge: # average gene expression of pathway (aep); # pathway activities classification (PAC); # Hub network classification (hubc); # filter via top ranked genes (FrSVM); # network smoothed t-statistic (stSVM). | protein-protein interaction network, biomarker discovery, classification, micoarray, gene expression profile, protein-protein interaction, gene expression, gene, biomarker |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24443376 | Free, Public | OMICS_02241 | SCR_005672 | 2026-02-07 02:06:54 | 0 | |||||||
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MAGMA Resource Report Resource Website 100+ mentions |
MAGMA (RRID:SCR_005757) | MAGMA | software resource | Software that utilizes a multiobjective evolutionary algorithm for genetic mapping. It is based on a the ECJ evolutionary software package written by Sean Luke and includes the Strength Pareto Evoluationary Algorithm Version 2 changes for multiobjective analysis. The code runs on any platform with Java Version 2. A genetic mapping project, typically implemented during a search for genes responsible for a disease, requires the acquisition of a set of data from each of a large number of individuals. This data set includes the values of multiple genetic markers. These genetic markers occur at discrete positions along the genome, which is a collection of one or more linear chromosomes. Typing the value of a marker in an individual carries a cost; one seeks to minimize the number of markers typed without excessively jeopardizing the probability of detecting an association between a marker and a disease phenotype. MAGMA is a project which employ''s a multiobjective evolutionary algorithm to solve this problem. | gene, genetic mapping, algorithm, genomics, single nucleotide polymorphism, population study, haplotype-block elucidation, java | has parent organization: SourceForge | Juvenile Diabetes Research Foundation | PMID:12875658 | Open unspecified license | nlx_149220 | SCR_005757 | Multiobjective Analyzer for Genetic Marker Acquisition, MAGMA: Multiobjective Analyzer for Genetic Marker Acquisition | 2026-02-07 02:06:50 | 415 | |||||
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ClueGO Resource Report Resource Website 1000+ mentions |
ClueGO (RRID:SCR_005748) | ClueGO | software resource | A Cytoscape plug-in that visualizes the non-redundant biological terms for large clusters of genes in a functionally grouped network. It can be used in combination with GOlorize. The identifiers can be uploaded from a text file or interactively from a network of Cytoscape. The type of identifiers supported can be easily extended by the user. ClueGO performs single cluster analysis and comparison of clusters. From the ontology sources used, the terms are selected by different filter criteria. The related terms which share similar associated genes can be combined to reduce redundancy. The ClueGO network is created with kappa statistics and reflects the relationships between the terms based on the similarity of their associated genes. On the network, the node colour can be switched between functional groups and clusters distribution. ClueGO charts are underlying the specificity and the common aspects of the biological role. The significance of the terms and groups is automatically calculated. ClueGO is easy updatable with the newest files from Gene Ontology and KEGG. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | statistical analysis, function, gene ontology, pathway, annotation, network, plugin, gene |
is listed by: Gene Ontology Tools is listed by: SoftCite is related to: Gene Ontology is related to: Cytoscape is related to: KEGG is related to: BioCarta Pathways has parent organization: National Institute of Health and Medical Research; Rennes; France |
National Institute of Health and Medical Research; Rennes; France ; Ville de Paris ; INCa ; Austrian Ministry for Science and Research ; BINII ; European Union 7FP 202230 |
PMID:19237447 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_149209 | SCR_005748 | 2026-02-07 02:06:50 | 2941 | ||||||
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GeneChip™ Scanner 3000 7G Resource Report Resource Website 1+ mentions |
GeneChip™ Scanner 3000 7G (RRID:SCR_016522) | instrument resource | Scanner for microarray analysis to scan next-generation higher-density arrays, including SNP arrays, tiling arrays for transcription and all-exon arrays for whole-genome analysis. | Instrument, microarray, analysis, scan, next, generation, array, whole, genome, gene, chip | Commercially available | https://www.thermofisher.com/document-connect/document-connect.html?url=https://assets.thermofisher.com/TFS-Assets%2FGSD%2FDatasheets%2Fgenechip_scanner_3000_datasheet.pdf | SCR_016522 | 2026-02-07 02:09:28 | 1 | ||||||||||
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ChIPXpress Resource Report Resource Website 1+ mentions |
ChIPXpress (RRID:SCR_006653) | ChIPXpress | software resource | A R package designed to improve ChIP-seq and ChIP-chip target gene ranking using publicly available gene expression data. It takes as input predicted transcription factor (TF) bound genes from ChIPx data and uses a corresponding database of gene expression profiles downloaded from NCBI GEO to rank the TF bound targets in order of which gene is most likely to be functional TF target. | gene expression, chip-seq, chip-chip, transcription factor, target gene, gene, gene expression profile |
is listed by: OMICtools is related to: Gene Expression Omnibus has parent organization: Bioconductor |
GNU General Public License, v2 or greater | OMICS_00516 | SCR_006653 | ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip data using publicly available gene expression profiles | 2026-02-07 02:07:14 | 2 | |||||||
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GREC Corpus Resource Report Resource Website 1+ mentions |
GREC Corpus (RRID:SCR_006719) | GREC | training set | A semantically annotated corpus of 240 MEDLINE abstracts (167 on the subject of E. coli species and 73 on the subject of the Human species) intended for training information extraction (IE) systems and/or resources which are used to extract events from biomedical literature. The corpus has been manually annotated with events relating to gene regulation by biologists. Each event is centered on either a verb (e.g. transcribe) or nominalized verb (e.g. transcription) and annotation consists of identifying, as exhaustively as possible, the structurally-related arguments of the verb or nominalized verb within the same sentence. Each event argument is then assigned the following information: * A semantic role from a fixed set of 13 roles which are tailored to the biomedical domain. * A biomedical concept type (where appropriate). The corpus in available for download in 2 formats: * A standoff format, based on the BioNLP'09 Shared Task format * An XML format, based on the GENIA event annotation format | annotation, information extraction, text mining, semantic role, semantic search, gene, computational linguistics, gene regulation |
is listed by: FORCE11 is related to: MEDLINE has parent organization: National Centre for Text Mining |
JISC | PMID:19852798 | Creative Commons Attribution-NonCommercial-ShareAlike License, v3 Unported, For Copyright of abstracts refer to PubMed. | nif-0000-06688 | SCR_006719 | Gene Event Regulation Corpus | 2026-02-07 02:07:15 | 3 | |||||
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Glimmer-MG Resource Report Resource Website 1+ mentions |
Glimmer-MG (RRID:SCR_011932) | Glimmer-MG | software resource | A software system for finding genes in environmental shotgun DNA sequences. | metagenomics, gene |
is listed by: OMICtools is related to: Glimmer has parent organization: University of Maryland; Maryland; USA |
Open unspecified license, OSI certified | OMICS_01487 | SCR_011932 | Glimmer-MG: Metagenomics Gene-Finding System, Gene Locator and Interpolated Markov ModelER - MetaGenomics | 2026-02-07 02:08:19 | 8 | |||||||
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3D Genome Resource Report Resource Website 10+ mentions |
3D Genome (RRID:SCR_017525) | service resource | Genome Browser for study of 3D genome organization and gene regulation and data visualization. Used to visualizing chromatin interaction data, browse other omics data such as ChIP-Seq or RNA-Seq for same genomic region, and gain complete view of both regulatory landscape and 3D genome structure for any given gene., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | 3D, genome, organization, gene, regulation, data, visualization, chromatin, interaction, omic, ChIPseq, RNAseq, regulatory, structure |
is related to: Encode has parent organization: Pennsylvania State University |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_017525 | 2026-02-07 02:10:04 | 20 | ||||||||||
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ENTROPY BLOCKER Resource Report Resource Website |
ENTROPY BLOCKER (RRID:SCR_000123) | ENTROPY BLOCKER | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software application aiming at identifying haplotype blocks. The likelihood of the data is calculated minus the model complexity. The resulting blocks have very low diversity and the linkage disequilibrium with SNP's outside the blocks is low. (entry from Genetic Analysis Software) | gene, genetic, genomic, r, ms-windows, linux | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154300, nlx_154581, SCR_007247 | SCR_000123 | R/ENTROPY BLOCKER, R/ENTROPY_BLOCKER | 2026-02-07 02:12:54 | 0 | |||||||
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POOLSCORE Resource Report Resource Website |
POOLSCORE (RRID:SCR_007514) | software resource, software application | Software program for analysis of case-control genetic association studies using allele frequency measurements on DNA pools (entry from Genetic Analysis Software) | gene, genetic, genomic, r | is listed by: Genetic Analysis Software | SCR_009373, nlx_154595, nlx_154087 | SCR_007514 | R/POOLSCORE | 2026-02-07 02:13:21 | 0 | |||||||||
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HAPLOCLUSTERS Resource Report Resource Website |
HAPLOCLUSTERS (RRID:SCR_007439) | HAPLOCLUSTERS | software resource, software application | Software program designed to detect excess haplotypes sharing in datasets consisting of case and control haplotypes. Excess haplotype sharing can be seen around disease loci in case samples since LD persists longer here than in the controls where LD is persisting only according to the relatedness of the individuals in the population, i.e. the age of the population. (entry from Genetic Analysis Software) | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
Aging | nlx_154014, biotools:haploclusters | https://bio.tools/haploclusters | SCR_007439 | 2026-02-07 02:14:33 | 0 | |||||||
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LDSUPPORT Resource Report Resource Website |
LDSUPPORT (RRID:SCR_007036) | software resource, software application | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix, linux | is listed by: Genetic Analysis Software | nlx_154427 | SCR_007036 | 2026-02-07 02:14:19 | 0 | ||||||||||
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BETA Resource Report Resource Website 100+ mentions |
BETA (RRID:SCR_007556) | BETA | software resource, software application | Software application for non-parametric linkage analysis using allele sharing in sib pairs (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix, sun | is listed by: Genetic Analysis Software | nlx_154241 | SCR_007556 | 2026-02-07 02:14:20 | 122 | |||||||||
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MAPCREATOR Resource Report Resource Website 1+ mentions |
MAPCREATOR (RRID:SCR_008001) | MAPCREATOR | software resource, software application | Software application to create gene maps using either radiation hybrid data or linkage data (entry from Genetic Analysis Software) | gene, genetic, genomic, perl | is listed by: Genetic Analysis Software | nlx_154455 | SCR_008001 | 2026-02-07 02:14:17 | 3 | |||||||||
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Graphical Overview of Linkage Disequilibrium Resource Report Resource Website 1000+ mentions |
Graphical Overview of Linkage Disequilibrium (RRID:SCR_007151) | GOLD | software resource, software application | Software package that provides a graphical summary of linkage disequilibrium in human genetic data. The graphical summary is well suited to the analysis of dense genetic maps, where contingency tables are cumbersome to interpret. An interface to the Simwalk2 application allows for the analysis of family data. | gene, genetic, genomic |
is listed by: Genetic Analysis Software has parent organization: University of Michigan; Ann Arbor; USA |
PMID:10842743 | nlx_154363 | SCR_007151 | 2026-02-07 02:14:20 | 2212 | ||||||||
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BMAPBUILDER Resource Report Resource Website 1+ mentions |
BMAPBUILDER (RRID:SCR_007264) | BMAPBUILDER | software resource, software application | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, java, ms-windows, macos, unix, linux | is listed by: Genetic Analysis Software | nlx_154084 | SCR_007264 | 2026-02-07 02:14:20 | 1 | |||||||||
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Xenopus Gene Collection Resource Report Resource Website 1+ mentions |
Xenopus Gene Collection (RRID:SCR_007023) | XGC | biomaterial supply resource, material resource | NIH initiative to support production of cDNA libraries, clones and 5'/3' sequences and to provide set of full-length (open reading frame) sequences and cDNA clones of expressed genes for Xenopus laevis and Xenopus tropicalis. Clones distribution is outsourced to for profit companies. Project concluded in September 2008. Resources generated by XGC are publicly accessible to biomedical research community. All sequences are deposited into GenBank.Corresponding clones are available through IMAGE clone distribution network. With conclusion of XGC project, GenBank records of XGC sequences will be frozen, without further updates. Since knowledge of what constitutes full-length coding region for some of genes and transcripts for which we have XGC clones will likely change in future, users planning to order XGC clones will need to monitor for these changes. Users can make use of genome browsers and gene-specific databases, such as UCSC Genome browser, NCBI's Map Viewer, and Entrez Gene, to view relevant regions of genome (browsers) or gene-related information (Entrez Gene). | est sequencing, expressed gene, frog, gene, adult, cdna, genomic, open reading frame, sequencing, stage, tag, xenopus laevis, xenopus tropicalis, sequence, expressed sequence tag, cdna, vector, cdna library, clone, 5'/3' sequence, frozen |
is listed by: One Mind Biospecimen Bank Listing is related to: One Mind Biospecimen Bank Listing is related to: ATCC is related to: GenBank is related to: Invitrogen Clones has parent organization: National Cancer Institute |
NIH Blueprint for Neuroscience Research ; NIH |
Free, Freely available | nif-0000-00224 | https://genecollections.nci.nih.gov/XGC/ | SCR_007023 | Xenopus Gene Collection | 2026-02-07 02:14:33 | 4 | |||||
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ETDT Resource Report Resource Website 1+ mentions |
ETDT (RRID:SCR_007576) | ETDT | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 5th,2023. Software application for TDT test on markers with more than two alleles using a logistic regression analysis. (entry from Genetic Analysis Software). | gene, genetic, genomic, c, ms-dos | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154303 | SCR_007576 | extended transmission/disequilibrium test | 2026-02-07 02:14:17 | 2 | |||||||
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Zebrafish Gene Collection Resource Report Resource Website 1+ mentions |
Zebrafish Gene Collection (RRID:SCR_007054) | ZGC | biomaterial supply resource, material resource | Part of zebrafish genome project. ZGC project to produce cDNA libraries, clones and sequences to provide complete set of full-length (open reading frame) sequences and cDNA clones of expressed genes for zebrafish. All ZGC sequences are deposited in GenBank and clones can be purchased from distributors of IMAGE consortium. With conclusion of ZGC project in September 2008, GenBank records of ZGC sequences will be frozen, without further updates. Since definition of what constitutes full-length coding region for some of genes and transcripts for which we have ZGC clones will likely change in future, users planning to order ZGC clones will need to monitor for these changes. Users can make use of genome browsers and gene-specific databases, such as UCSC Genome browser, NCBI's Map Viewer, and Entrez Gene, to view relevant regions of genome (browsers) or gene-related information (Entrez Gene). | cdna library, clone, sequence, full-length open reading frame, cdna clone, frozen, fish, gene, genetic, genome, genomic |
is listed by: One Mind Biospecimen Bank Listing is related to: One Mind Biospecimen Bank Listing is related to: NIDDK Information Network (dkNET) is related to: Mammalian Gene Collection is related to: GenBank is related to: ATCC has parent organization: National Cancer Institute |
NIH Blueprint for Neuroscience Research | Free, Freely available | nif-0000-00567 | https://genecollections.nci.nih.gov/ZGC/ | SCR_007054 | Zebrafish Gene Collection | 2026-02-07 02:14:15 | 1 | |||||
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TRANSMIT Resource Report Resource Website 50+ mentions |
TRANSMIT (RRID:SCR_007571) | TRANSMIT | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. Software application that tests for association between genetic marker and disease by examining the transmission of markers from parents to affected offspring. The main features which differ from other similar programs are: (1) It can deal with transmission of multi-locus haplotypes, even if phase is unknown, and (2) Parental genotypes may be unknown. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, unix | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154100 | SCR_007571 | 2026-02-07 02:14:34 | 50 |
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