Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
SCAN Resource Report Resource Website 500+ mentions |
SCAN (RRID:SCR_005185) | SCAN | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. A large-scale database of genetics and genomics data associated to a web-interface and a set of methods and algorithms that can be used for mining the data in it. The database contains two categories of single nucleotide polymorphism (SNP) annotations: # Physical-based annotation where SNPs are categorized according to their position relative to genes (intronic, inter-genic, etc.) and according to linkage disequilibrium (LD) patterns (an inter-genic SNP can be annotated to a gene if it is in LD with variation in the gene). # Functional annotation where SNPs are classified according to their effects on expression levels, i.e. whether they are expression quantitative trait loci (eQTLs) for that gene. SCAN can be utilized in several ways including: (i) queries of the SNP and gene databases; (ii) analysis using the attached tools and algorithms; (iii) downloading files with SNP annotation for various GWA platforms. . eQTL files and reported GWAS from NHGRI may be downloaded., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | single nucleotide polymorphism, copy number variation, annotation, genetics, genomics, genome-wide association study, gene, linkage disequilibrium, function, expression quantitative trait loci, expression, quantitative trait loci, chromosome, chromosome region, affymetrix, cerebellum, parietal, liver |
is listed by: OMICtools is listed by: SoftCite has parent organization: University of Chicago; Illinois; USA |
NIMH R01MH090937; NHLBI U01HL084715; NIGMS U01GM61393; NIDDK P60 DK20595; NCI P50 CA125183 |
PMID:25818895 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00181 | SCR_005185 | SCAN: SNP and CNV Annotation Database, SCAN - SNP and CNV Annotation Database | 2026-02-14 02:06:25 | 740 | |||||
|
HaploReg Resource Report Resource Website 1000+ mentions |
HaploReg (RRID:SCR_006796) | HaploReg | data or information resource, database | HaploReg is a tool for exploring annotations of the noncoding genome at variants on haplotype blocks, such as candidate regulatory SNPs at disease-associated loci. Using linkage disequilibrium (LD) information from the 1000 Genomes Project, linked SNPs and small indels can be visualized along with their predicted chromatin state in nine cell types, conservation across mammals, and their effect on regulatory motifs. HaploReg is designed for researchers developing mechanistic hypotheses of the impact of non-coding variants on clinical phenotypes and normal variation. | chromatin state, conservation, regulatory motif, alteration, variant, chromatin, motif, annotation, genome, variation, genome-wide association study, refsnp, refseq gene, snp, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Broad Institute |
NHGRI R01-HG004037; NHGRI RC1-HG005334; NSF 0644282 |
PMID:22064851 | biotools:HaploReg, nlx_151407 | http://compbio.mit.edu/HaploReg https://bio.tools/HaploReg |
SCR_006796 | 2026-02-14 02:06:27 | 1004 | ||||||
|
ProSAS Resource Report Resource Website 1+ mentions |
ProSAS (RRID:SCR_007876) | ProSAS | data or information resource, database | This database provides a unified resource to analyze the effects of alternative splicing events on the structure of the resulting protein isoforms. ProSAS comprehensively annotates protein structures for several Ensembl genomes and alternative transcripts can be analyzed on the protein structure and protein function level using the intuitive user interface of the database. Users can search based on Ensembl gene or Ensembl transcript ids, Gene descriptions, Uniprot gene names, Genes matching patterns, Swissprot/Uniprot identifiers or Affymetrix probeset ids. |
is listed by: SoftCite has parent organization: Ludwig-Maximilians-University; Munich; Germany |
SCR_007876 | Protein Structure and Alternative Splicing | 2026-02-14 02:06:32 | 1 | ||||||||||
|
Maestro Resource Report Resource Website 50+ mentions |
Maestro (RRID:SCR_016748) | data or information resource, portal | Software tool for all purpose molecular modeling environment. Maestro is the portal to all of Schrödinger's computational technology. Helps researchers organize and analyze data. | molecular, modeling, environment, computation, data, analyze, organize |
is listed by: SoftCite has parent organization: Schrodinger |
Commercially available, Trial available | SCR_016748 | 2026-02-14 02:05:15 | 79 | ||||||||||
|
Blender Resource Report Resource Website 1000+ mentions |
Blender (RRID:SCR_008606) | data or information resource, database | Blender is the free open source 3D content creation suite, available for all major operating systems under the GNU General Public License. Because of the overwhelming success of the first open movie project, Ton Roosendaal, the Blender Foundation''s chairman, has established the Blender Institute. This now is the permanent office and studio to more efficiently organize the Blender Foundation goals, but especially to coordinate and facilitate Open Projects related to 3D movies, games or visual effects. | FASEB list |
is listed by: SoftCite is related to: NeuroMorph |
nif-0000-31943 | SCR_008606 | Blender | 2026-02-14 02:06:43 | 2220 | |||||||||
|
Google Scholar Resource Report Resource Website 10000+ mentions |
Google Scholar (RRID:SCR_008878) | Google Scholar | data or information resource, database | Google Scholar provides a simple way to broadly search for scholarly literature. From one place, you can search across many disciplines and sources: articles, theses, books, abstracts and court opinions, from academic publishers, professional societies, online repositories, universities and other web sites. Google Scholar helps you find relevant work across the world of scholarly research. Features of Google Scholar * Search diverse sources from one convenient place * Find articles, theses, books, abstracts or court opinions * Locate the complete document through your library or on the web * Learn about key scholarly literature in any area of research How are documents ranked? Google Scholar aims to rank documents the way researchers do, weighing the full text of each document, where it was published, who it was written by, as well as how often and how recently it has been cited in other scholarly literature. * Publishers - Include your publications in Google Scholar * Librarians - Help patrons discover your library''s resources | literature |
is used by: Writefull is listed by: SoftCite is parent organization of: Google Scholar Blog |
nlx_151304 | SCR_008878 | 2026-02-14 02:06:36 | 38796 | |||||||||
|
CEAS Resource Report Resource Website 100+ mentions |
CEAS (RRID:SCR_010946) | CEAS | software resource | Integrates many useful tools to simplify ChIP-chip analysis for biologists., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools is listed by: SoftCite |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00802 | SCR_010946 | 2026-02-14 02:02:07 | 397 | |||||||||
|
lumi Resource Report Resource Website 100+ mentions |
lumi (RRID:SCR_012781) | lumi | software resource | Software that provides an integrated solution for the Illumina microarray data analysis. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Bioconductor |
biotools:lumi, OMICS_00770 | https://bio.tools/lumi | SCR_012781 | 2026-02-14 02:02:16 | 318 | ||||||||
|
Ringo Resource Report Resource Website 10+ mentions |
Ringo (RRID:SCR_012973) | Ringo | software resource | Software package that facilitates the primary analysis of ChIP-chip data. |
is listed by: OMICtools is listed by: SoftCite has parent organization: Bioconductor |
OMICS_00809 | SCR_012973 | 2026-02-14 02:02:45 | 38 | ||||||||||
|
Google Resource Report Resource Website 100+ mentions |
Google (RRID:SCR_017097) | commercial organization | American multinational technology company that specializes in internet related services and products, which include online advertising technologies, search engine, cloud computing, software, and hardware. Considered one of Big Four technology companies, alongside Amazon, Apple and Facebook. | technology, company, internet, service, product, search, engine, cloud, computing, software, hardware, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite is parent organization of: golang |
grid.420451.6, Crossref funder ID: 100006785, ISNI, Wikidata: Q95, biotools:Google | https://ror.org/00njsd438 https://bio.tools/Google |
SCR_017097 | Google LLC | 2026-02-14 02:03:14 | 332 | ||||||||
|
ASPicDB Resource Report Resource Website 1+ mentions |
ASPicDB (RRID:SCR_002102) | ASPicDB | data or information resource, database | A database to access reliable annotations of the alternative splicing pattern of human genes, obtained by ASPic algorithm (Castrignano et al. 2006), and to the functional annotation of predicted isoforms. Users may select and extract specific sets of data related to genes, transcripts and introns fulfilling a combination of user-defined criteria. Several tabular and graphical views of the results are presented, providing a comprehensive assessment of the functional implication of alternative splicing in the gene set under investigation. ASPicDB also includes information on tissue-specific splicing patterns of normal and cancer cells, based on available EST data and their library source annotation. | annotation, splicing pattern, gene, transcript, intron, protein, variant, alternative splicing, splicing, blast, exon, u2, u12, isoform |
is listed by: OMICtools is listed by: SoftCite has parent organization: University of Bari; Bari; Italy |
Normal, Cancer | PMID:21051348 PMID:18388144 |
Free, Freely available | OMICS_01882 | http://srv00.ibbe.cnr.it/ASPicDB/ | SCR_002102 | Alternative Splicing Prediction Data Base, ASPicDB - A Database tool for alternative splicing analysis | 2026-02-14 02:06:04 | 7 | ||||
|
SAM Resource Report Resource Website 100+ mentions |
SAM (RRID:SCR_010951) | software resource | Software for genomic expression data mining using a statistical technique for finding significant genes in a set of microarray experiments. | genomic expression, data mining, finding significant genes, microarray experiments, |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite is related to: pysam has parent organization: Stanford University; Stanford; California |
Commercial use requires license, Registration required | OMICS_01314, OMICS_00779, SCR_011888 | https://sources.debian.org/src/r-cran-samr/ | SCR_010951 | SAM: Significance Analysis of Microarrays, Significance Analysis of Microarrays | 2026-02-14 02:07:43 | 235 | |||||||
|
Web of Science Resource Report Resource Website 10+ mentions |
Web of Science (RRID:SCR_022706) | data or information resource, database | Database of bibliographic citations of multidisciplinary areas that covers various journals of medical, scientific, and social sciences including humanities.Publisher independent global citation database. | Clarivate, publisher independent, global citation database, bibliographic citations of multidisciplinary areas, various journals | is listed by: SoftCite | Free | SCR_022706 | Web of Knowledge | 2026-02-14 02:06:50 | 18 | |||||||||
|
Ensembl Genome Browser Resource Report Resource Website 1000+ mentions |
Ensembl Genome Browser (RRID:SCR_013367) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17,2022. Genome databases for vertebrates and other eukaryotic species. Analysis and annotation maintained on current data.Distribution of analysis to other bioinformatics laboratories. Ensembl concentrates on vertebrate genomes, but other groups have adapted system for use with plant and fungal genomes (see Powered by Ensembl list on website). |
is listed by: SoftCite has parent organization: Ensembl |
European Bioinformatics Institute ; Wellcome Trust Sanger Institute |
THIS RESOURCE IS NO LONGER IN SERVICE. | nif-0000-30518 | http://uswest.ensembl.org/index.html | SCR_013367 | 2026-02-14 02:06:43 | 1179 | ||||||||
|
RAxML Resource Report Resource Website 10000+ mentions |
RAxML (RRID:SCR_006086) | RAxML | software application, data processing software, data analysis software, software resource | Software program for phylogenetic analyses of large datasets under maximum likelihood. | phylogeny, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: RAxML Next Generation works with: PAML |
PMID:24451623 PMID:16928733 PMID:15608047 DOI:10.1093/bioinformatics/btu033 |
GNU General Public License | biotools:raxml, OMICS_02242 | https://bio.tools/raxml https://sources.debian.org/src/raxml/ |
SCR_006086 | Randomized Axelerated Maximum Likelihood | 2026-02-15 09:19:08 | 12473 | |||||
|
Galaxy Resource Report Resource Website 5000+ mentions |
Galaxy (RRID:SCR_006281) | Galaxy | organization portal, portal, data analysis service, service resource, production service resource, data or information resource, analysis service resource | Open, web-based platform providing bioinformatics tools and services for data intensive genomic research. Platform may be used as a service or installed locally to perform, reproduce, and share complete analyses. Galaxy automatically tracks and manages data provenance and provides support for capturing the context and intent of computational methods. Galaxy Community has created Galaxy instances in many different forms and for many different applications including Galaxy servers, cloud services that support Galaxy instances, and virtual machines and containers that can be easily deployed for your own server.The Galaxy team is a part of BX at Penn State, and the Biology and Mathematics and Computer Science departments at Emory University.Training Infrastructure as a Service (TIaaS) is a service offered by some UseGalaxy servers to specifically support training use cases. | bioinformatics, workflow, analysis, data sharing, visualization, cloud, genomics, metagenomics, next-generation sequencing, platform, data set, genaddiction tool |
is used by: Nebula lists: PathwayMatcher is listed by: OMICtools is listed by: 3DVC is listed by: Debian is listed by: SoftCite is related to: ABrowse is related to: TRAMS is related to: Stem Cell Commons is related to: Stem Cell Discovery Engine is related to: CardioVascular Research Grid (CVRG) is related to: rQuant is related to: SnpEff is related to: Binding and Expression Target Analysis is related to: PIPE-CLIP is related to: Stem Cell Discovery Engine is related to: Computational Genomics Analysis Tools is related to: SpliceTrap is related to: SMAGEXP is related to: CandiMeth is related to: ewas-galaxy is related to: CLIP-Explorer is related to: Galactic Circos is related to: Tool recommender system in Galaxy is related to: NanoGalaxy is related to: Cistrome is related to: Training Infrastructure as a Service has parent organization: Pennsylvania State University is parent organization of: kmer-SVM works with: Deeptools |
Huck Institutes for the Life Sciences ; Pennsylvania Department of Health ; NSF DBI0850103; NHGRI HG004909; NHGRI HG005133; NHGRI HG005542; Institute for CyberScience at Pennsylvania State University ; Pennsylvania ; USA ; Johns Hopkins University |
PMID:20738864 PMID:20069535 PMID:16169926 |
Free, Freely available | nlx_151896, OMICS_01141 | https://usegalaxy.org/ https://sources.debian.org/src/galaxy/ |
SCR_006281 | The Galaxy Project, Galaxy Project | 2026-02-15 09:19:23 | 5473 | ||||
|
RNAhybrid Resource Report Resource Website 100+ mentions |
RNAhybrid (RRID:SCR_003252) | RNAhybrid | data analysis service, software resource, service resource, production service resource, analysis service resource | Software tool for finding the minimum free energy hybridization of a long and a short RNA. The hybridization is performed in a kind of domain mode, i.e., the short sequence is hybridized to the best fitting part of the long one. The tool is primarily meant as a means for microRNA target prediction. | microrna, target prediction, free energy, rna, bio.tools |
is listed by: OMICtools is listed by: 3DVC is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Bielefeld University; North Rhine-Westphalia; Germany |
PMID:15383676 DOI:10.1261/rna.5248604 |
Free, Available for download, Freely available | OMICS_00416, biotools:rnahybrid, nif-0000-31412 | https://bio.tools/rnahybrid https://sources.debian.org/src/rnahybrid/ |
SCR_003252 | 2026-02-15 09:18:28 | 477 | ||||||
|
GeneChip Operating Software Resource Report Resource Website 500+ mentions |
GeneChip Operating Software (RRID:SCR_003408) | GCOS | software application, sequence analysis software, data processing software, software resource, data analysis software | Affymetrix has recently released a new software for the acquisition, management, and analysis of gene expression data. The new GeneChip Operating Software (GCOS) platform enables researchers to perform gene expression, SNP mapping and resequencing analysis with integrated data management and scalable client server configurations. * Compatible with additional Affymetrix analysis software such as Data Mining Tool (DMT) and GeneChip DNA Analysis Software (GDAS) * Supports Gene Expression, Resequencing and Genotyping Applications * Baseline Comparison Analysis Input: Affymetrix .DAT file Output: Affymetrix files (.CEL, .CHP, .RPT, .EXP, .TXT) Availability: The Core Facility has a copy of GCOS, as well as an older version of the Affymetrix software, Microarray Suite (MAS), available for use upon request. | gene expression, snp mapping, resequencing, analysis, genotyping, platform, software, comparison, analysis |
is listed by: Biositemaps is listed by: SoftCite has parent organization: Scripps Research Institute |
Free, Available for download, Freely available | nif-0000-33019 | https://www.thermofisher.com/us/en/home/life-science/microarray-analysis/microarray-analysis-instruments-software-services/microarray-analysis-software/genechip-operating-software-service-pack-2-software-update.html | SCR_003408 | GeneChip Operating Software (GCOS), DNA Array Core Facility GeneChip Operating Software, DNA Array Core Facility GeneChip Operating Software (GCOS) | 2026-02-15 09:18:30 | 649 | ||||||
|
IMOD Resource Report Resource Website 1000+ mentions |
IMOD (RRID:SCR_003297) | IMOD | software application, image processing software, data processing software, software resource, source code, image analysis software | A free, cross-platform set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and display of the image files. IMOD 4.1.8 Is Now Available for Linux, Windows, and Mac OS X | electron microscopy, magnetic resonance, tomographic reconstruction, reconstruction, segmentation, 3d volume |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: SoftCite has parent organization: University of Colorado Boulder; Colorado; USA |
NCRR ; NIGMS ; NIBIB |
PMID:27444392 | Free, Available for download, Freely available | nif-0000-31686 | http://www.nitrc.org/projects/imod | SCR_003297 | IMOD - 3D Reconstruction and Analysis | 2026-02-15 09:18:32 | 1585 | ||||
|
Jmol Resource Report Resource Website 100+ mentions |
Jmol (RRID:SCR_003796) | Jmol | software application, d visualization software, standalone software, software resource | An open-source Java viewer for chemical structures in 3D with features for chemicals, crystals, materials and biomolecules. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems and features an applet, application, and systems integration component. | chemical, crystal, material, biomolecule, java |
is used by: Glyco3D is listed by: SoftCite has parent organization: SourceForge |
PMID:28472503 PMID:28316648 |
GNU Lesser General Public License, Acknowledgement requested | nlx_158093 | SCR_003796 | Jmol: an open-source Java viewer for chemical structures in 3D | 2026-02-15 09:18:37 | 233 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that NIF has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on NIF then you can log in from here to get additional features in NIF such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into NIF you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
