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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
GeMoMa Resource Report Resource Website 100+ mentions |
GeMoMa (RRID:SCR_017646) | software application, simulation software, software resource | Software tool as homology based gene prediction program that predicts gene models in target species based on gene models in evolutionary related reference species. Utilizes amino acid sequence conservation, intron position conservation, and RNA-seq data to accurately predict protein-coding transcripts. Supports combination of predictions based on several reference species allowing to transfer high quality annotation of different reference species to target species. | Homology, based, gene, prediction, model, target, evolutionary, related, reference, species, sequence, conservation, intron, position, RNAseq, data, protein, coding, transcript, bio.tools |
is listed by: bio.tools is listed by: Debian works with: GUSHR |
PMID:31020559 | Free, Available for download, Freely available | biotools:gemoma | https://bio.tools/gemoma | SCR_017646 | Gene Model Mapper | 2026-07-27 09:35:32 | 135 | ||||||
|
MB-GAN Resource Report Resource Website 1+ mentions |
MB-GAN (RRID:SCR_019289) | software application, simulation software, software resource | Software tool as deep learning simulation framework for simulating realistic microbiome data. Can automatically learn from given microbial abundances and compute simulated abundances that are indistinguishable from it. | Metagenomics, deep learning, generative adversarial network, microbiome data simulation, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Texas at Dallas; Texas; USA |
DOI:10.1101/863977 | Free, Available for download, Freely available | biotools:mb-gan | https://bio.tools/mb-gan | SCR_019289 | Microbiome Simulation via Generative Adversarial Network | 2026-07-27 09:35:55 | 1 | ||||||
|
MetaBase Resource Report Resource Website 50+ mentions |
MetaBase (RRID:SCR_001762) | MB | database, data or information resource, wiki, narrative resource | User-contributed list of biological databases available on the internet. Currently there are 1,801 entries, each describing a different database. The databases are described in a semi-structured way by using templates and entries can carry various user comments and annotations. Entries can be searched, listed or browsed by category. The site uses the same MediaWiki technology that powers Wikipedia, The Mediawiki system allows users to participate on many different levels, ranging from authors and editors to curators and designers. MetaBase aims to be a flexible, user-driven (user-created) resource for the biological database community. The main focuses of MetaBase are: * As a basic requirement, MB contains a list of databases, URLs and descriptions of the most commonly used biological databases currently available on the internet. * The system should be flexible, allowing users to contribute, update and maintain the data in different ways. * In the future we aim to generate more communication between the database developer and user communities. | biological, mediawiki, biology, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: Genome Research Foundation |
MKE - Ministry of Knowledge Economy | PMID:22139927 | Free, Freely available | biotools:metabase, nif-0000-10293 | https://bio.tools/metabase | http://biodatabase.org/index.php?title=Main_Page&oldid=8972 | SCR_001762 | MetaBase (MB) | 2026-07-28 09:40:16 | 81 | |||
|
SPP Resource Report Resource Website 1+ mentions |
SPP (RRID:SCR_001790) | software application, software resource, data analysis software, data processing software | R analysis and processing package for Illumina platform Chip-Seq data. | chip seq data, illummina, r package, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
NHGRI U01HG004258; NIGMS R01GM082798; NCRR UL1RR024920 |
DOI:10.1038/nbt.1508 | Free, Available for download, Freely available | OMICS_00425, biotools:spp | https://bio.tools/spp | https://sites.google.com/a/brown.edu/bioinformatics-in-biomed/spp-r-from-chip-seq | SCR_001790 | SPP Package | 2026-07-28 09:40:16 | 9 | ||||
|
myExperiment Resource Report Resource Website 10+ mentions |
myExperiment (RRID:SCR_001795) | myExperiment | software application, service resource, workflow software, community building portal, data or information resource, data repository, database, software resource, data processing software, storage service resource, portal | Community repository and virtual research environment where scientists can safely publish their workflows and experiment plans, share them with groups and find and use those of others. Workflows, other digital objects and collections (called Packs) can be swapped, sorted and searched. It supports Linked data, has a SPARQL Endpoint and REST API and is based on an open source Ruby on Rails codebase. Scientific workflows in various formats can be uploaded. Specific support is provided for Taverna workflows for which the system displays relevant metadata, components and visual previews, that are retrieved directly from workflow files. Version history for workflows is collected. This feature allows the contributor to keep previous versions of the workflow available, when the latest one is uploaded. This brings additional benefit for the users by allowing them to view the development stages of the workflow towards its latest implementation. | workflow, pipeline, platform, component, data sharing, publish, digital object, experimental method, workflow management, virtual research environment, collaborative computing, taverna workflow workbench, bioinformatics, web service, bio.tools |
is listed by: FORCE11 is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Taverna is related to: Workflow4Ever is related to: Biocatalogue - The Life Science Web Services Registry has parent organization: University of Southampton; Southampton; United Kingdom has parent organization: University of Manchester; Manchester; United Kingdom has parent organization: University of Oxford; Oxford; United Kingdom |
JISC ; Microsoft Technical Computing Initiative ; EPSRC |
PMID:20501605 | Free, Freely available | nif-0000-10309, r3d100010473, biotools:myexperiment | https://www.force11.org/node/4638, https://bio.tools/myexperiment | SCR_001795 | my experiment | 2026-07-28 09:40:25 | 23 | ||||
|
Chilibot: Gene and Protein relationships from MEDLINE Resource Report Resource Website 10+ mentions |
Chilibot: Gene and Protein relationships from MEDLINE (RRID:SCR_001705) | Chilibot | service resource, data or information resource, data analysis service, database, production service resource, analysis service resource | Data analysis service that searches PubMed literature database (abstracts) about specific relationships between proteins, genes, or keywords using a NLP-based text-mining approach. The results are returned as a graph. The synonym database used in Chilibot is available, without fee, for academic use only. Several different search methods are supported including: * searching for relationship between two genes, proteins or keywords * searching for relationships between many genes, proteins, or keywords * searching for relationships between two lists of genes, proteins, or keywords Advanced options include: * Automated hypothesis generation (graph) * Restricting context using keywords * Providing your own synonyms * Modifying synonyms provided by Chilibot * Color coding nodes with gene expression values * Special search: modulation | drug, gene, literature, natural language processing, protein, text-mining, network, keyword, biological concept, graph, bio.tools |
is listed by: OMICtools is listed by: 3DVC is listed by: bio.tools is listed by: Debian is related to: PubMed has parent organization: University of Tennessee Health Science Center; Tennessee; USA |
PHS DA-03977 | PMID:15473905 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10196, OMICS_01176, biotools:chilibot | https://bio.tools/chilibot | SCR_001705 | Chilibot - Mining PubMed for relationships | 2026-07-28 09:40:15 | 30 | ||||
|
Addgene Resource Report Resource Website 10000+ mentions |
Addgene (RRID:SCR_002037) | service resource, data or information resource, organization portal, material storage repository, storage service resource, portal | Non-profit plasmid repository dedicated to helping scientists around the world share high-quality plasmids. Facilitates archiving and distributing DNA-based research reagents and associated data to scientists worldwide. Repository contains over 65,000 plasmids, including special collections on CRISPR, fluorescent proteins, and ready-to-use viral preparations. There is no cost for scientists to deposit plasmids, which saves time and money associated with shipping plasmids themselves. All plasmids are fully sequenced for validation and sequencing data is openly available. We handle the appropriate Material Transfer Agreements (MTA) with institutions, facilitating open exchange and offering intellectual property and liability protection for depositing scientists. Furthermore, we curate free educational resources for the scientific community including a blog, eBooks, video protocols, and detailed molecular biology resources. | RIN, Resource Information Network, plasmid, molecular biology, sequence alignment, repository, bio.tools, FASEB list, RRID Community Authority |
uses: GenomeCompiler is used by: NIF Data Federation is used by: NIDDK Information Network (dkNET) is used by: Structural Genomics Consortium is used by: ZCre is listed by: One Mind Biospecimen Bank Listing is listed by: DataCite is listed by: re3data.org is listed by: bio.tools is listed by: Debian is listed by: Resource Information Network is related to: zfishbook is related to: GenomeCompiler is related to: Phoenix is related to: Integrated Manually Extracted Annotation is related to: Genetic Tools Atlas is parent organization of: Vector Database |
Fees collected from plasmid sales support operation of the repository | DOI:10.1093/nar/gku893 | Free (deposit of plasmids), Limited (Some available to academic and non-profits, For-profit entities, Commercial license), Material Transfer Agreement, Non-commercial, Acknowledgement required, Copyrighted, For informational purposes only, Commercial with written consent, The community can contribute to this resource | ISNI: 0000 0004 5912 0787, Wikidata: Q4681063, grid.482682.2, biotools:Addgene, nif-0000-11872 | https://ror.org/01nn1pw54, https://bio.tools/Addgene | SCR_002037 | Addgene Repository, Addgene Plasmid Database | 2026-07-28 09:40:19 | 50586 | |||||
|
Candida Genome Database Resource Report Resource Website 100+ mentions |
Candida Genome Database (RRID:SCR_002036) | CGD, CGD LOCUS, CGD REF | service resource, data or information resource, data repository, database, storage service resource | Database of genetic and molecular biological information about Candida albicans. Contains information about genes and proteins, descriptions and classifications of their biological roles, molecular functions, and subcellular localizations, gene, protein, and chromosome sequence information, tools for analysis and comparison of sequences and links to literature information. Each CGD gene or open reading frame has an individual Locus Page. Genetic loci that are not tied to DNA sequence also have Locus Pages. Provides Gene Ontology, GO, to all its users. Three ontologies that comprise GO (Molecular Function, Cellular Component, and Biological Process) are used by multiple databases to annotate gene products, so that this common vocabulary can be used to compare gene products across species. Development of ontologies is ongoing in order to incorporate new information. Data submissions are welcome. | protein, chromosome, classification, gene, genome, candidiasis, thrush, yeast, yeast gene, yeast genome, candida albicans, candida glabrata, data analysis service, biological role, molecular function, subcellular localization, chromosome sequence, bio.tools, FASEB list |
is used by: NIF Data Federation is listed by: bio.tools is listed by: Debian is related to: AmiGO is related to: ASPGD is related to: Gene Ontology has parent organization: Stanford University School of Medicine; California; USA |
NIDCR DE015873 | PMID:19808938 | Free, Available for download, Freely available | nif-0000-02634, biotools:cgd, r3d100010617 | https://bio.tools/cgd | SCR_002036 | 2026-07-28 09:40:19 | 472 | |||||
|
InteroPorc Resource Report Resource Website 1+ mentions |
InteroPorc (RRID:SCR_002067) | InteroPorc | software application, service resource, data analysis software, data or information resource, data analysis service, database, data processing software, software resource, source code, production service resource, analysis service resource | Automatic prediction tool to infer protein-protein interaction networks, it is applicable for lots of species using orthology and known interactions. The interoPORC method is based on the interolog concept and combines source interaction datasets from public databases as well as clusters of orthologous proteins (PORC) available on Integr8. Users can use this page to ask InteroPorc for all species present in Integr8. Some results are already computed and users can run InteroPorc to investigate any other species. Currently, the following databases are processed and merged (with datetime of the last available public release for each database used): IntAct, MINT, DIP, and Integr8. | orthology, prediction, protein interaction, tool, sequenced genome, proteinprotein interaction, inferred interaction, molecular interaction, interaction, protein, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Integr8 : Access to complete genomes and proteomes is related to: IntAct is related to: MINT is related to: Database of Interacting Proteins (DIP) is related to: PSICQUIC Registry has parent organization: CEA; Gif sur Yvette; France |
European Union FELICS 021902 RII3; Marie Curie Fellowship ; French National Agency of Research ANR Biosys06_134823 SULFIRHOM; French Atomic Energy Commission |
PMID:18508856 | Open unspecified license, Acknowledgement requested | nif-0000-20816, biotools:interoporc | https://bio.tools/interoporc | SCR_002067 | InteroPorc: Automatic molecular interaction predictions, Automatic molecular interaction predictions | 2026-07-28 09:40:32 | 6 | ||||
|
SNVer Resource Report Resource Website 50+ mentions |
SNVer (RRID:SCR_002061) | software application, software resource, data analysis software, data processing software | Statistical software tool for calling common and rare variants in analysis of pool or individual next-generation sequencing data. This software is optimized for analysis of whole-exome sequencing data and whole-genome sequencing data. | statistical analysis software, sequencing, dna, whole-exome, whole-genome, variant, bio.tools |
lists: SAMTOOLS is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:21813454 | Free, Available for download, Freely available | OMICS_00076, biotools:snver | https://sourceforge.net/projects/snver/, https://bio.tools/snver | SCR_002061 | 2026-07-28 09:40:20 | 51 | |||||||
|
GATK Resource Report Resource Website 10000+ mentions |
GATK (RRID:SCR_001876) | GATK | software application, data analysis software, software resource, data processing software, software library, software toolkit | A software package to analyze next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. This software library makes writing efficient analysis tools using next-generation sequencing data very easy, and second it's a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner. (entry from Genetic Analysis Software) | gene, genetic, genomic, next-generation resequencing, bio.tools |
is used by: Halvade Somatic is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: SnpEff is related to: GATK HaplotypeCaller is related to: GATK VariantFiltration has parent organization: Broad Institute |
PMID:21478889 | Free, Available for download, Freely available | nlx_154324, OMICS_00286, biotools:gatk | http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit, https://bio.tools/gatk | SCR_001876 | Genome Analysis ToolKit | 2026-07-28 09:40:17 | 16663 | |||||
|
ChIPSeq Peak Finder Resource Report Resource Website 1+ mentions |
ChIPSeq Peak Finder (RRID:SCR_002081) | software application, software resource, data analysis software, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE, documented on April 12, 2017. A software tool to find peaks from ChIPSeq data generated from the Solexa/Illumina platform., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | chipseq, sequencing, dna, analysis, solexa, illumina |
is listed by: OMICtools is listed by: Debian has parent organization: Genome Institute of Singapore; Singapore; Singapore |
PMID:27863463 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00434 | https://sources.debian.org/src/chip-seq/ | SCR_002081 | ChIPSeq Toolbox | 2026-07-28 09:40:20 | 1 | ||||||
|
JGI Genome Portal Resource Report Resource Website 500+ mentions |
JGI Genome Portal (RRID:SCR_002383) | data or information resource, organization portal, department portal, portal | Portal providing access to all JGI genomic databases and analytical tools, sequencing projects and their status, search for and download assemblies and annotations of sequenced genomes, and interactively explore those genomes and compare them with other sequenced microbes, fungi, plants or metagenomes using specialized systems tailored to each particular class of organisms. The Department of Energy (DOE) Joint Genome Institute (JGI) is a national user facility with massive-scale DNA sequencing and analysis capabilities dedicated to advancing genomics for bioenergy and environmental applications. Beyond generating tens of trillions of DNA bases annually, the Institute develops and maintains data management systems and specialized analytical capabilities to manage and interpret complex genomic data sets, and to enable an expanding community of users around the world to analyze these data in different contexts over the web. | gene, computation, genome, genomics, model organism, assembly, annotation, sequenced genome, metagenome, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: DOE Joint Genome Institute is parent organization of: Takifugu rubripes Genome |
Department of Energy | PMID:24225321 PMID:22110030 |
nif-0000-21230, SCR_004706, OMICS_01654, biotools:jgi_genome_portal, nlx_69965 | http://genome.jgi-psf.org, https://bio.tools/jgi_genome_portal | http://genome.jgi-psf.org/ | SCR_002383 | JGI Genome Portal, DOE Joint Genome Institute Genome Portal | 2026-07-28 09:40:24 | 865 | |||||
|
Ensembl Resource Report Resource Website 10000+ mentions |
Ensembl (RRID:SCR_002344) | data or information resource, database | Collection of genome databases for vertebrates and other eukaryotic species with DNA and protein sequence search capabilities. Used to automatically annotate genome, integrate this annotation with other available biological data and make data publicly available via web. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species. | collection, genome, dataset, database, vertebrate, eukaryotic, DNA, protein, sequence, search, automaticly, annotate, data, bio.tools, FASEB list |
is used by: NIF Data Federation is used by: Animal QTLdb is used by: ChannelPedia is used by: Blueprint Epigenome is used by: HmtPhenome lists: Ensembl Covid-19 is listed by: OMICtools is listed by: Biositemaps is listed by: re3data.org is listed by: LabWorm is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Ensembl Genomes is related to: GermOnline is related to: CandiSNPer is related to: Human Splicing Finder is related to: NGS-SNP is related to: Sanger Mouse Resources Portal is related to: DECIPHER is related to: Ensembl Genomes is related to: PeptideAtlas is related to: AnimalTFDB is related to: Bgee: dataBase for Gene Expression Evolution is related to: FlyMine is related to: Rat Gene Symbol Tracker is related to: UniParc at the EBI is related to: go-db-perl is related to: UniParc is related to: g:Profiler is related to: RIKEN integrated database of mammals is related to: VBASE2 is related to: p300db is related to: ShinyGO has parent organization: European Bioinformatics Institute has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom is parent organization of: Ensembl Metazoa is parent organization of: Ensembl Variation is parent organization of: Pre Ensembl is parent organization of: Variant Effect Predictor is parent organization of: Ensembl Bacteria is parent organization of: Ensembl Plants is parent organization of: Ensembl Fungi is parent organization of: Ensembl Protists is parent organization of: Ensembl Genome Browser works with: Genotate works with: CellPhoneDB works with: Open Regulatory Annotation Database works with: Database of genes related to Repeat Expansion Diseases works with: TarBase |
Wellcome Trust ; EMBL ; European Union ; FP7 ; FP6 ; MRC ; NHGRI ; BBSRC |
PMID:24316576 PMID:23203987 |
nif-0000-21145, OMICS_01647, biotools:ensembl, r3d100010228 | https://bio.tools/ensembl, https://sources.debian.org/src/ensembl/, https://doi.org/10.17616/R39K5B | SCR_002344 | ENSEMBL | 2026-07-28 09:40:24 | 11652 | ||||||
|
dbSNP Resource Report Resource Website 5000+ mentions |
dbSNP (RRID:SCR_002338) | dbSNP | service resource, data or information resource, data repository, database, storage service resource | Database as central repository for both single base nucleotide substitutions and short deletion and insertion polymorphisms. Distinguishes report of how to assay SNP from use of that SNP with individuals and populations. This separation simplifies some issues of data representation. However, these initial reports describing how to assay SNP will often be accompanied by SNP experiments measuring allele occurrence in individuals and populations. Community can contribute to this resource. | insertion, polymorphism, short, deletion, single, nucleotide, genetic, variation, genomics, genotype, disease, allele, microsatellite, marker, multinucleotide, heterozygous, sequence, gold standard, bio.tools |
is used by: ExAc is used by: GEMINI is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: OMICtools is listed by: re3data.org is listed by: bio.tools is listed by: Debian is related to: Ensembl Variation is related to: GWAS Central is related to: TopoSNP is related to: GWAS Central has parent organization: NCBI has parent organization: National Human Genome Research Institute works with: Open Regulatory Annotation Database |
NLM | PMID:21154707 | Free, Freely available | nif-0000-02734, biotools:dbsnp, OMICS_00264, r3d100010652 | http://www.ncbi.nlm.nih.gov/projects/SNP/, https://bio.tools/dbsnp, https://doi.org/10.17616/R3XG81 | SCR_002338 | dbSNP: Database for Short Genetic Variations, Entrez SNP - Single Nucleotide Polymorphism, SNV Database, NCBI SNV Database, NCBI Short Genetic Variations Database, NCBI Short Genetic Variations, NCBI Single Nucleotide Polymorphism, Entrez SNP, dbSNP, NCBI Short Genetic Variations (SNV) database | 2026-07-28 09:40:24 | 8619 | ||||
|
VAAST Resource Report Resource Website 10+ mentions |
VAAST (RRID:SCR_002179) | VAAST, VAAST 2 | software application, data analysis software, sequence analysis software, software resource, data processing software, standalone software | A probabilistic search tool for identifying damaged genes and their disease-causing variants in personal genome sequences. VAAST combines elements of phylogenetic conservation, amino acid substitution, and aggregative approaches to variant prioritization into a single unified likelihood-framework that allows users to accurately identify damaged genes and deleterious variants. The software can score both coding (SNV, indel and splice site) and non-coding variants (SNV), evaluating the cumulative impact of both types of variants simultaneously. It can identify rare variants causing rare genetic diseases and can also use both rare and common variants to identify genes responsible for common diseases. | sequence analysis software, genetic, variant classifier, amino acid substitution, disease, genome interpretation, variant prioritization, disease gene prioritization, genomic variation, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian is related to: Opal Research has parent organization: Yandell Lab Portal |
PMID:23836555 PMID:21700766 |
Free, Freely available | nlx_154686, SciRes_000138, biotools:vaast, OMICS_02134 | https://bio.tools/vaast | SCR_002179 | Variant Annotation Analysis and Search Tool, Variant Annotation Analysis & Search Tool | 2026-07-28 09:40:35 | 30 | |||||
|
SEEK Resource Report Resource Website 10+ mentions |
SEEK (RRID:SCR_002651) | SEEK | software application, service resource, data repository, data access protocol, software resource, data management software, data processing software, source code, web service, data storage software, storage service resource | An open-source, web-based platform and suite of software tools for for sharing heterogeneous scientific research datasets, models or simulations, processes and research outcomes - and collaborations between scientists. It preserves associations between them, along with information about the people and organizations involved. Underpinning SEEK is the ISA infrastructure, a standard format for describing how individual experiments are aggregated into wider studies and investigations. Within SEEK, ISA has been extended and is configurable to allow the structure to be used outside of Biology. SEEK is incorporating semantic technology allowing sophisticated queries over the data, yet without getting in the way of your users. Access to the RESTful API to access the data within SEEK is available. | data sharing, data set, systems biology, standard exchange format, metadata standard, data management, data citation, publishing software, bio.tools |
is listed by: OMICtools is listed by: FORCE11 is listed by: bio.tools is listed by: Debian is related to: ISA Infrastructure for Managing Experimental Metadata is related to: RightField has parent organization: University of Manchester; Manchester; United Kingdom has parent organization: Heidelberg Institute for Theoretical Studies; Heidelberg; Germany |
BBSRC ; BMBF |
PMID:21943917 | Free, Available for download, Freely available | nlx_156079, OMICS_01012, biotools:seek | http://www.force11.org/node/4806, https://bio.tools/seek | SCR_002651 | SEEK Platform, SEEK for Science | 2026-07-28 09:40:29 | 33 | ||||
|
SAFA Footprinting Software Resource Report Resource Website 1+ mentions |
SAFA Footprinting Software (RRID:SCR_002707) | SAFA | software application, software resource, data analysis software, data processing software | A software package that anayzes the structral details of RNA molecules through rapid quantification of a footprinting gel. By automating many of the steps involved in gel analysis, approximately one entire gel with thousands of bands can be quantified in less than 10 minutes using SAFA. In general, all the automated features have a manual override, such that even difficult or exceptional gels can be analyzed with the package. | footprint, gel, data analysis, software, RNA, RNA folding, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Simtk.org |
PMID:15701734 PMID:18772866 |
Free, Available for download, Freely available | nif-0000-23336, biotools:safa | https://bio.tools/safa | SCR_002707 | Semi-Automated Footprinting Analysis Software | 2026-07-28 09:40:29 | 8 | |||||
|
pyxnat Resource Report Resource Website 1+ mentions |
pyxnat (RRID:SCR_002574) | pyxnat | software library, software toolkit, software resource | Software Python library that relies on the REST API provided by the XNAT platform since its 1.4 version. XNAT is an extensible database for neuroimaging data. The main objective is to ease communications with an XNAT server to plug-in external tools or python scripts to process the data. | computed tomography, magnetic resonance, pet, spect, python |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is related to: XNAT - The Extensible Neuroimaging Archive Toolkit |
European Union | PMID:22654752 | Free, Available for download, Freely available | nlx_155977 | https://sources.debian.org/src/python-pyxnat/ | SCR_002574 | pyxnat: XNAT in Python | 2026-07-28 09:40:38 | 1 | ||||
|
ParaView Resource Report Resource Website 500+ mentions |
ParaView (RRID:SCR_002516) | ParaView | software application, data analysis software, software resource, data processing software, data visualization software | Open source, multi platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data using qualitative and quantitative techniques. The data exploration can be done interactively in 3D or programmatically using ParaView's batch processing capabilities. ParaView was developed to analyze extremely large datasets using distributed memory computing resources. It can be run on supercomputers to analyze datasets of terascale as well as on laptops for smaller data. | magnetic resonance |
uses: VTK is used by: Spine Detection and Extraction is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is related to: SIGEN has parent organization: Kitware |
Free, Available for download, Freely available | nlx_155917 | http://www.nitrc.org/projects/paraview, https://sources.debian.org/src/paraview/ | SCR_002516 | 2026-07-28 09:40:37 | 595 |
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 dkNET Resources search. From here you can search through a compilation of resources used by dkNET and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that dkNET 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 dkNET then you can log in from here to get additional features in dkNET 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 dkNET 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.
The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
Email: info_at_ dknet.org
