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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Transporter Classification Database Resource Report Resource Website 100+ mentions |
Transporter Classification Database (RRID:SCR_004490) | TCDB, TC | storage service resource, source code, software resource, service resource, production service resource, data analysis software, data repository, data analysis service, data or information resource, data processing software, software application, analysis service resource, database | Curated, relational database containing sequence, classification, structural, functional and evolutionary information about transport systems from variety of living organisms based on IUBMB-approved transporter classification (TC) system. Descriptions, TC numbers, and examples of over 600 families of transport proteins are provided. TC system is analogous to Enzyme Commission (EC) system for classification of enzymes, except that it incorporates both functional and phylogenetic information. TCDB users may submit their own sequenced proteins and descriptions for inclusion into database. The software tools used are all freely available for download. These programs are used for analysis of Protein and DNA sequences. Programs require UNIX server to run. | membrane transport, protein sequence, transporter, bio.tools, FASEB list |
is recommended by: National Library of Medicine is listed by: bio.tools is listed by: Debian has parent organization: University of California at San Diego; California; USA |
NIGMS GM1077402 | PMID:19022853 PMID:16381841 |
Free, Freely available | nlx_47724, biotools:tcdb | https://bio.tools/tcdb | SCR_004490 | Transporter Classification Database | 2026-08-06 09:26:09 | 311 | ||||
|
SMART Resource Report Resource Website 5000+ mentions |
SMART (RRID:SCR_005026) | SMART | software resource, service resource, data access protocol, production service resource, data analysis service, data or information resource, web service, analysis service resource, database | Software tool for identification and annotation of genetically mobile domains and analysis of domain architectures. | extracellular, gene, genetic, genetically, genome, architecture, chromatin, domain, mobile, phyletic, protein, proteome, signaling, structure, taxonomic, tertiary, bio.tools, FASEB list |
is used by: Mutation Annotation and Genomic Interpretation is listed by: bio.tools is listed by: Debian is related to: Eukaryotic Linear Motif is related to: Conserved Domain Database is related to: GOTaxExplorer has parent organization: EMBL - Bork Group |
European Union | PMID:18978020 PMID:16381859 PMID:14681379 PMID:10592234 PMID:9847187 PMID:9600884 |
Free, Freely available | nif-0000-03471, biotools:smart | http://smart.embl-heidelberg.de/, https://bio.tools/smart | SCR_005026 | Simple Modular Architecture Research Tool | 2026-08-06 09:26:19 | 6760 | ||||
|
NCBI BLAST Resource Report Resource Website 10000+ mentions |
NCBI BLAST (RRID:SCR_004870) | BLAST | sequence analysis software, software resource, data access protocol, data analysis software, web service, data processing software, software application | Web search tool to find regions of similarity between biological sequences. Program compares nucleotide or protein sequences to sequence databases and calculates statistical significance. Used for identifying homologous sequences. | genome, similarity, sequence, nucleotide, protein, gene, data, bio.tools |
is used by: MITE-Tracker is used by: Cello2Go is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: G-BLASTN is related to: genBlastA has parent organization: NCBI is required by: RelocaTE works with: Whole Genome Shotgun (WGS) Project works with: BLASTClust works with: MOLE-BLAST works with: Genotyping |
National Library of Medicine | PMID:16845079 PMID:18440982 |
Free, Freely available, Tutorial available | OMICS_01436, nlx_84530, biotools:blast | http://blast.ncbi.nlm.nih.gov, https://bio.tools/blast, https://sources.debian.org/src/ncbi-blast+/ | SCR_004870 | NCBI Basic Local Alignment Search Tool, NCBI BLAST, Basic Local Alignment Search Tool, BLAST | 2026-08-06 09:26:15 | 15381 | ||||
|
ngsTools Resource Report Resource Website 50+ mentions |
ngsTools (RRID:SCR_005489) | ngsTools | data analysis software, software application, software resource, data processing software | A collection of software programs for population genetics analyses from NGS (Next-Generation Sequencing) data, taking into account its statistical uncertainty. The methods implemented in these programs do not rely on SNP (Single Nucleotide Polymorphism) or genotype calling, and are particularly suitable for low sequencing depth data. | java, next-generation sequencing, population, genetics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24458950 | GNU General Public License, v3, Acknowledgement requested | OMICS_02248, biotools:ngstools | https://bio.tools/ngstools | SCR_005489 | 2026-08-06 09:26:25 | 53 | ||||||
|
SolexaQA Resource Report Resource Website 100+ mentions |
SolexaQA (RRID:SCR_005421) | SolexaQA | sequence analysis software, software resource, data analysis software, data processing software, data visualization software, software application | Software package to calculate sequence quality statistics and create visual representations of data quality for Illumina's second-generation sequencing technology. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:20875133 | Acknowledgement requested | biotools:solexaqa, OMICS_01078 | https://bio.tools/solexaqa | SCR_005421 | 2026-08-06 09:26:24 | 291 | ||||||
|
PHAge Search Tool Resource Report Resource Website 100+ mentions |
PHAge Search Tool (RRID:SCR_005184) | PHAST | data set, service resource, production service resource, data analysis service, data or information resource, analysis service resource | A web server designed to rapidly and accurately identify, annotate and graphically display prophage sequences within bacterial genomes or plasmids. It accepts either raw DNA sequence data or partially annotated GenBank formatted data and rapidly performs a number of database comparisons as well as phage cornerstone feature identification steps to locate, annotate and display prophage sequences and prophage features. Relative to other prophage identification tools, PHAST is up to 40 times faster and up to 15% more sensitive. It is also able to process and annotate both raw DNA sequence data and Genbank files, provide richly annotated tables on prophage features and prophage quality and distinguish between intact and incomplete prophage. PHAST also generates downloadable, high quality, interactive graphics that display all identified prophage components in both circular and linear genomic views. Databases available for download include Virus DB, Prophage and virus DB, Bacteria DB, and PHAST result DB. Pre-calculated genomes for viewing are also available. | prophage sequence, genome, prophage, sequence, bacterial genome, plasmid, dna sequence, graph, phage, annotate, virus, nucleotide sequence, fasta, annotated genome, genbank, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Alberta; Alberta; Canada |
PMID:21672955 | Acknowledgement requested | biotools:phast, OMICS_00180 | https://bio.tools/phast | SCR_005184 | PHAST - PHAge Search Tool | 2026-08-06 09:26:22 | 225 | |||||
|
FLASH Resource Report Resource Website 1000+ mentions |
FLASH (RRID:SCR_005531) | FLASh | sequence analysis software, software resource, data analysis software, data processing software, software application | Open source software tool to merge paired-end reads from next-generation sequencing experiments. Designed to merge pairs of reads when original DNA fragments are shorter than twice length of reads. Can improve genome assemblies and transcriptome assembly by merging RNA-seq data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: shovill is related to: CLIP-Explorer has parent organization: Johns Hopkins University; Maryland; USA |
NLM R01 LM006845; NIGMS R01 GM083873; NHGRI R01 HG006677 |
PMID:21903629 | Free, Available for download, Freely available | biotools:flash, OMICS_01047 | https://sourceforge.net/projects/flashpage/files/, https://bio.tools/flash, https://sources.debian.org/src/flash/ | SCR_005531 | Fast Length Adjustment of SHort reads, Fast Length Adjustment of Short reads | 2026-08-06 09:26:27 | 2175 | ||||
|
CLIPZ Resource Report Resource Website 10+ mentions |
CLIPZ (RRID:SCR_005755) | CLIPZ | service resource, production service resource, data analysis service, data or information resource, analysis service resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 20,2019.Database and analysis environment for experimentally determined binding sites of RNA-binding proteins. It supports the automatic functional annotation of short reads resulting primarily from crosslinking and immunoprecipitation experiments (CLIP) performed with RNA-binding proteins in order to identify the binding sites of these proteins. The functional annotation could be also applied to short reads resulting from other types of experiments such as mRNA-Seq, Digital Gene Expression, small RNA cloning, etc. The platform enables visualization and mining of individual data sets as well as analysis involving multiple experimental data sets. The platform can support collaborative projects involving multiple users and groups of users as well as public and private datasets. | rna-binding protein, binding site, protein, functional annotation, cross-linking and immunoprecipitation, short read, mrna-seq, digital gene expression, small rna cloning, visualization, mining, analysis, post-transcriptional regulatory element, genome, transcript, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SIB Swiss Institute of Bioinformatics has parent organization: University of Basel; Basel; Switzerland |
PMID:21087992 | THIS RESOURCE IS NO LONGER IN SERVICE. | OMICS_02256, biotools:clipz | https://bio.tools/clipz | SCR_005755 | 2026-08-06 09:26:29 | 20 | ||||||
|
Sybil Resource Report Resource Website 10+ mentions |
Sybil (RRID:SCR_005593) | Sybil | database, data or information resource, software resource | A web-based software package for comparative genomics. | comparative genomics, genome, synteny, protein cluster, protein, gene, genomic region, synteny gradient, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:22121156 | OMICS_00945, biotools:sybil | https://bio.tools/sybil | SCR_005593 | Sybil: Web-based software for comparative genomics | 2026-08-06 09:26:27 | 37 | ||||||
|
959 Nematode Genomes Resource Report Resource Website 1+ mentions |
959 Nematode Genomes (RRID:SCR_006068) | NematodeGenomes | wiki, narrative resource, data or information resource | A collaborative wiki that collates information on completed, ongoing and planned genome and transcriptome sequencing projects on species from phylum Nematoda. The intention is to encourage genome sequencing across the diversity of the phylum Nematoda. Wiki includes: * Published complete nematode genomes: A dynamically generated table of all species for which the genome is published. * Nematode species with genomes in progress: A dynamically generated table of all species for which a genome project is underway. Users may add species to the list * Proposed nematode genome projects: To propose a species for genome sequencing, edit its species page, and set the genome project status to proposed. * BLAST server: Search a number of the nematode-genomes-in-progress with genes of your choice. Currently there are 12 draft genomes available... * Genomes with Data available: Genomes with data available for download. Users may add more data URLs to strain pages or update the URLs. | nematode, genome, genome sequencing, transcriptome sequencing, blast, genomics, sequencing, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: nematodes.org has parent organization: University of Edinburgh; Scotland; United Kingdom |
NERC | PMID:22058131 | nlx_151473, biotools:959_nematode_genomes | https://bio.tools/959_nematode_genomes | SCR_006068 | NematodeGenomes | 2026-08-06 09:26:29 | 2 | |||||
|
MMMDB - Mouse Multiple tissue Metabolome DataBase Resource Report Resource Website 1+ mentions |
MMMDB - Mouse Multiple tissue Metabolome DataBase (RRID:SCR_006064) | MMMDB | service resource, production service resource, data analysis service, data or information resource, analysis service resource, database | MMMDB, Mouse Multiple tissue Metabolome DataBase, is a freely available metabolomic database containing a collection of metabolites measured from multiple tissues from single mice. The datases are collected using a single instrument and not integrated from literatures, which is useful for capturing the holistic overview of large metabolomic pathway. Currently data from cerabra, cerebella, thymus, spleen, lung, liver, kidney, heart, pancreas, testis, and plasma are provided. Non-targeted analyses were performed by capillary electropherograms time-of-flight mass spectrometry (CE-TOFMS) and, therefore, both identified metabolites and unknown (without matched standard) peaks were uploaded to this database. Not only quantified concentration but also processed raw data such as electropherogram, mass spectrometry, and annotation (such as isotope and fragment) are provided. | metabolite, metabolome, cerabra, cerebella, thymus, spleen, lung, liver, kidney, heart, pancreas, testis, plasma, metabolomic pathway, capillary electropherograms time-of-flight mass spectrometry, electropherogram, mass spectrometry, annotation, isotope, fragment, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:22139941 | Free | nlx_151467, biotools:mmmdb | https://bio.tools/mmmdb | SCR_006064 | Mouse Multiple tissue Metabolome DataBase | 2026-08-06 09:26:29 | 1 | |||||
|
InterEvol database Resource Report Resource Website 10+ mentions |
InterEvol database (RRID:SCR_006054) | InterEvol | software resource, service resource, production service resource, data analysis service, data or information resource, analysis service resource, database | InterEvol database is designed for the analysis of co-evolution events at the interface of known structures of hetero- and homo-oligomers. The database can be search and analyzed through 3 interconnected levels of analysis: * From a Keyword or the PDB entry of a complex, you can browse: ** structural homologs for every chain in other complexes ** structural interologs for every interface ** retrieve pre-computed sequence alignments in diverse species * From 1 or 2 sequences of interacting partners: ** build 2 multiple sequence alignments with the same species ordered in each ** query the InterEvol database with alignments using profile-profile comparison method * Visualize structure vs sequence alignment at the complex interface ** A dedicated Pymol plugin is provided ** Alignment views in Pymol are interactively restricted to the residues selected at the interface | structure, evolution, protein complex, interface, protein complex, sequence alignment, plug in, protein structure, visualization, pymol plugin, structural homolog, structural interolog, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) has parent organization: CEA; Gif sur Yvette; France |
Commissariat a lEnergie Atomique ; ANR HPGenVar |
PMID:22053089 | Free and open to all users - no login requirement | nlx_151453, biotools:interevol | https://bio.tools/interevol | SCR_006054 | 2026-08-06 09:26:32 | 10 | |||||
|
ICEberg Resource Report Resource Website 50+ mentions |
ICEberg (RRID:SCR_006026) | ICEberg | service resource, production service resource, data analysis service, data or information resource, analysis service resource, database | ICEberg is an integrated database that provides comprehensive information about integrative and conjugative elements (ICEs) found in bacteria. ICEs are conjugative self-transmissible elements that can integrate into and excise from a host chromosome. An ICE contains three typical modules, integration and excision, conjugation, and regulation modules, that collectively promote vertical inheritance and periodic lateral gene flow. Many ICEs carry likely virulence determinants, antibiotic-resistant factors and/or genes coding for other beneficial traits. ICEberg offers a unique, highly organized, readily explorable archive of both predicted and experimentally supported ICE-relevant data. It currently contains details of 428 ICEs found in representatives of 124 bacterial species, and a collection of >400 directly related references. A broad range of similarity search, sequence alignment, genome context browser, phylogenetic and other functional analysis tools are readily accessible via ICEberg. ICEberg will facilitate efficient, multidisciplinary and innovative exploration of bacterial ICEs and be of particular interest to researchers in the broad fields of prokaryotic evolution, pathogenesis, biotechnology and metabolism. The ICEberg database will be maintained, updated and improved regularly to ensure its ongoing maximum utility to the research community. | dna, protein, sequence, chromosome, element, gene, similarity search, sequence alignment, genome, phylogenetic, functional analysis, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: Shanghai Jiao Tong University; Shanghai; China |
National Natural Science Foundation of China 973 program 2009CB118901; National Natural Science Foundation of China 973 program 2012CB721002; National Natural Science Foundation of China 863 program 2011BAD23B05-3; Ministry of Science and Technology China ; Ministry of Education China NCET-10-0572; Shanghai Jiaotong University ; Shanghai Municipality ; Action Medical Research SP4255; Innovation Fellowship ; East Midlands Development Agency |
PMID:22009673 | nlx_151424, biotools:iceberg | https://bio.tools/iceberg | SCR_006026 | ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria | 2026-08-06 09:26:30 | 77 | |||||
|
Europe PubMed Central Resource Report Resource Website 500+ mentions |
Europe PubMed Central (RRID:SCR_005901) | Europe PMC, UKPMC | software resource, data access protocol, web service, data or information resource, bibliography, database | Free access to biomedical literature resources including all of PubMed and PubMed Central, agricultural abstracts (from AGRICOLA), over 4 million international life science patents abstracts, National Health Service (NHS) clinical guidelines, and is supplemented with Chinese Biological Abstracts and the Citeseer database. As well as powerful search of abstracts and full text articles, it also includes: * article citations and sort order based on citation count * data citations mined from full text articles * links to and from related databases and institutional repositories * a tool to create bibliographies linked to your ORCID * named entity recognition of keywords and text-mining-based applications showcased in Europe PMC Labs * Tools for recipients of grants from one of the Europe PMC funders to deposit full-text manuscripts and link them to those specific grants. * Web services for programmatic access to all the above bibliographic information and 50,000 grants. * Search by publication date, relevance, or the number of times an article has been cited. * Links to public databases such as UniProt, Protein Data Bank (PDBe), and the European Nucleotide Archive (ENA) are provided. * Through textmining technologies, you can highlight and browse keywords such as gene names, organisms and diseases. * Search 40,000 biomedical research grants awarded to the 18,000 PIs supported by the Europe PMC funders. * Roadtest new tools based on Europe PMC content in Europe PMC labs. * In Europe PMC plus, PIs supported by the Europe PMC funders can link grants to publication information, view article citation and download statistics, and submit manuscripts. | biomedical, literature, publication, health, life science, patent, clinical guideline, grant, text mining, author identification, archiving, open access, gold standard, bio.tools, bio.tools, FASEB list |
uses: EvidenceFinder uses: BioLexicon is listed by: FORCE11 is listed by: Debian is listed by: bio.tools is related to: PubMed is related to: PubMed Central is related to: AGRICOLA is related to: ORCID - Open Researcher and Contributor ID is related to: EvidenceFinder has parent organization: European Bioinformatics Institute has parent organization: Mimas has parent organization: National Centre for Text Mining is parent organization of: EvidenceFinder |
Wellcome Trust WT098231 | PMID:21062818 | Free, The community can contribute to this resource | nlx_149472, biotools:europe_pmc, biotools:ukpmc | https://bio.tools/ukpmc, https://bio.tools/europe_pmc | http://ukpmc.ac.uk/ | SCR_005901 | UK PubMed Central | 2026-08-06 09:26:28 | 505 | |||
|
pickgene Resource Report Resource Website |
pickgene (RRID:SCR_001331) | pickgene | data analysis software, software application, software resource, data processing software | Software for adaptive Gene Picking for Microarray Expression Data Analysis. | microarray, gene expression, differential expression, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02007, biotools:pickgene | https://bio.tools/pickgene | SCR_001331 | 2026-08-06 09:25:22 | 0 | |||||||
|
VCFtools Resource Report Resource Website 1000+ mentions |
VCFtools (RRID:SCR_001235) | data management software, software application, software resource | Software package for working with VCF files. Used to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.Implements various utilities for processing Variant Call Format files, including validation, merging, comparing. Provides general Perl API. | perl, genetic variation, variant call format, software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:21653522 DOI:10.1093/bioinformatics/btr330 |
Free, Available for download, Freely available | OMICS_02105, biotools:vcftools, SCR_012092, OMICS_05112 | https://bio.tools/vcftools, https://sources.debian.org/src/vcftools/ | http://vcftools.sourceforge.net/ | SCR_001235 | Variant Call Format Tools | 2026-08-06 09:25:21 | 4095 | |||||
|
ShortFuse Resource Report Resource Website 1+ mentions |
ShortFuse (RRID:SCR_001107) | sequence analysis software, software resource, data analysis software, data processing software, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. A software package with tools for identifying fusion transcripts from RNA-Seq data. It is written in C++, and has dependencies on packages from Python 2. | fusion transcripts, rna, sequence data, python 2, c++, sequence analysis software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:21330288 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:shortfuse, OMICS_01355 | https://bio.tools/shortfuse | SCR_001107 | 2026-08-06 09:25:19 | 1 | |||||||
|
metahdep Resource Report Resource Website |
metahdep (RRID:SCR_001225) | metahdep | data analysis software, software application, software resource, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software tools for meta-analysis in the presence of hierarchical (and/or sampling) dependence, including with gene expression studies. | differential expression, microarray, gene expression, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:19648140 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:metahdep, OMICS_02121 | https://bio.tools/metahdep | SCR_001225 | metahdep - Hierarchical Dependence in Meta-Analysis | 2026-08-06 09:25:21 | 0 | |||||
|
globaltest Resource Report Resource Website 10+ mentions |
globaltest (RRID:SCR_001256) | globaltest | sequence analysis software, software resource, data analysis software, data processing software, software application | A software package that tests groups of covariates (or features) for association with a response variable. The package implements the test with diagnostic plots and multiple testing utilities, along with several functions to facilitate the use of this test for gene set testing of GO and KEGG terms. | differential expression, go, microarray, one channel, pathway, bio.tools |
uses: KEGG is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: Bioconductor |
PMID:34046931 | Free, Available for download, Freely available | biotools:globaltest, OMICS_02084 | https://bio.tools/globaltest | SCR_001256 | 2026-08-06 09:25:21 | 30 | ||||||
|
DSRC Resource Report Resource Website 1+ mentions |
DSRC (RRID:SCR_001005) | DSRC | data management software, software application, software resource | An application designed for compression of data files containing reads from DNA sequencing in FASTQ format. Its main features include multithreaded compression of FASTQ output, python and C++ libraries, and support for lossy IDs compression. | fastq, dna sequence, compression, multithread, data management software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:21252073 | Free, Available as binary, Available as source code | biotools:dsrc, OMICS_00955 | https://bio.tools/dsrc | SCR_001005 | DNA Sequence Reads Compression, DNA Sequence Reads Compression (DSRC) | 2026-08-06 09:25:18 | 1 |
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 RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that RRID 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 RRID then you can log in from here to get additional features in RRID 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 RRID 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.