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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Rat Genome Database (RGD) Resource Report Resource Website 100+ mentions |
Rat Genome Database (RGD) (RRID:SCR_006444) | RGD | data or information resource, data repository, database, service resource, storage service resource | Database for genetic, genomic, phenotype, and disease data generated from rat research. Centralized database that collects, manages, and distributes data generated from rat genetic and genomic research and makes these data available to scientific community. Curation of mapped positions for quantitative trait loci, known mutations and other phenotypic data is provided. Facilitates investigators research efforts by providing tools to search, mine, and analyze this data. Strain reports include description of strain origin, disease, phenotype, genetics, immunology, behavior with links to related genes, QTLs, sub-strains, and strain sources. | RIN, Resource Information Network, mouse, rat, human, gene, qtl, marker, map, strain, sequence, est, genome, ontology, pathway, comparative genomics, physiology, phenotype, disease, model organism, proteomics, function, genetic, genomic, variation, immunology, behavior, knockout, inbred rat strain, mutant, congenic rat, recombinant inbred rat, data analysis service, organism supplier, genotype, gold standard, FASEB list, RRID Community Authority |
uses: InterMOD is used by: ChannelPedia is used by: Resource Identification Portal is used by: DisGeNET is used by: Integrated Animals is used by: NIH Heal Project is recommended by: Resource Identification Portal is listed by: re3data.org is listed by: InterMOD is listed by: Resource Information Network is affiliated with: InterMOD is related to: Rat Gene Symbol Tracker is related to: MPO is related to: NIF Data Federation is related to: MONARCH Initiative is related to: Vertebrate Trait Ontology is related to: Biositemaps is related to: One Mind Biospecimen Bank Listing is related to: AmiGO is related to: OMICtools is related to: re3data.org is related to: Integrated Manually Extracted Annotation is related to: OntoMate has parent organization: Medical College of Wisconsin; Wisconsin; USA is parent organization of: Diabetes Disease Portal is parent organization of: Rat Strain Ontology is parent organization of: Rat Strain Ontology is parent organization of: Renal Disease Portal is organization facet of: Alliance of Genome Resources |
NHLBI | PMID:23434633 PMID:18996890 PMID:17151068 |
Free, Freely available | nif-0000-00134, r3d100010417, OMICS_01660 | https://doi.org/10.17616/R3WK60 | SCR_006444 | , Rat Genome Database, RGD | 2026-09-05 06:25:53 | 280 | ||||
|
FlyBase Resource Report Resource Website 1000+ mentions |
FlyBase (RRID:SCR_006549) | FB | data or information resource, data repository, database, organism-related portal, portal, service resource, storage service resource, topical portal | Database of Drosophila genetic and genomic information with information about stock collections and fly genetic tools. Gene Ontology (GO) terms are used to describe three attributes of wild-type gene products: their molecular function, the biological processes in which they play a role, and their subcellular location. Additionally, FlyBase accepts data submissions. FlyBase can be searched for genes, alleles, aberrations and other genetic objects, phenotypes, sequences, stocks, images and movies, controlled terms, and Drosophila researchers using the tools available from the "Tools" drop-down menu in the Navigation bar. | RIN, Resource Information Network, mutant, gene, genome, blast, genotype, phenotype, allele, sequence, stock, image, movie, controlled term, video resource, image collection, life-cycle, genome, expression, rna-seq, genetics, drosophilidae, bio.tools, FASEB list, RRID Community Authority |
is used by: NIF Data Federation is used by: Resource Identification Portal is used by: PhenoGO is used by: Integrated Animals is used by: Drososhare is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: Resource Information Network is related to: FlyMine is related to: Virtual Fly Brain is related to: AmiGO is related to: Drosophila melanogaster Exon Database is related to: HomoloGene is related to: UniParc at the EBI is related to: UniParc is related to: Gene Ontology is related to: NIH Data Sharing Repositories is related to: GBrowse is related to: Integrated Manually Extracted Annotation is related to: PhenoGO has parent organization: Harvard University; Cambridge; United States has parent organization: University of Cambridge; Cambridge; United Kingdom has parent organization: Indiana University; Indiana; USA has parent organization: University of New Mexico; New Mexico; USA is parent organization of: Drosophila anatomy and development ontologies is parent organization of: Fly Taxonomy is parent organization of: FlyBase Controlled Vocabulary is parent organization of: Drosophila Development Ontology is organization facet of: Alliance of Genome Resources |
Indiana Genomics Initiative ; MRC ; NIH Blueprint for Neuroscience Research ; NIHGRI P41 HG000739; NSF |
PMID:24234449 PMID:22127867 PMID:18948289 PMID:18641940 PMID:18160408 PMID:17099233 PMID:16381917 PMID:15608223 PMID:12519974 PMID:11752267 PMID:11465064 PMID:9847148 PMID:9399806 PMID:9045212 PMID:8594600 PMID:8578603 PMID:7937045 PMID:7925011 |
nif-0000-00558, r3d100010591, OMICS_01649, biotools:flybase | https://bio.tools/flybase, https://doi.org/10.17616/R3903Q | http://flybase.net | SCR_006549 | flybase A Drosophila Genomic and Genetic Database, FlyBase: A Database of Drosophila Genes and Genomes, FLYBASE, FlyBase: A Database of Drosophila Genes & Genomes, FB | 2026-09-05 06:25:56 | 4234 | ||||
|
Decombinator Resource Report Resource Website 10+ mentions |
Decombinator (RRID:SCR_006732) | data analysis software, data processing software, software application, software resource, software toolkit | Software suite for analysis of T cell receptor repertoire data. Used for fast, efficient analysis of T cell receptor (TcR) repertoire samples, designed to be accessible to those with no previous programming experience. | Python, t-cell receptor sequence, t-cell receptor, sequence, deep sequencing, TCR repertoires, repertoire data, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University College London; London; United Kingdom |
PMID:23303508 PMID:32853330 |
Free, Available for download, Freely available | biotools:decombinator, OMICS_00001 | https://github.com/innate2adaptive/Decombinator, https://bio.tools/decombinator | SCR_006732 | Decombinator v2.2, Decombinator v4.0.3 | 2026-09-05 06:26:00 | 32 | ||||||
|
Pseudomonas Genome Database Resource Report Resource Website 500+ mentions |
Pseudomonas Genome Database (RRID:SCR_006590) | PseudoCAP | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Database of peer-reviewed, continually updated annotation for the Pseudomonas aeruginosa PAO1 reference strain genome expanded to include all Pseudomonas species to facilitate cross-strain and cross-species genome comparisons with high quality comparative genomics. The database contains robust assessment of orthologs, a novel ortholog clustering method, and incorporates five views of the data at the sequence and annotation levels (Gbrowse, Mauve and custom views) to facilitate genome comparisons. Other features include more accurate protein subcellular localization predictions and a user-friendly, Boolean searchable log file of updates for the reference strain PAO1. The current annotation is updated using recent research literature and peer-reviewed submissions by a worldwide community of PseudoCAP (Pseudomonas aeruginosa Community Annotation Project) participating researchers. If you are interested in participating, you are invited to get involved. Many annotations, DNA sequences, Orthologs, Intergenic DNA, and Protein sequences are available for download. | gene, genome, annotation, localization, prokaryote, pseudomonas aeruginosa, sequence, subcellular, cystic fibrosis, ortholog, annotation, dna sequence, intergenic dna, protein sequence, bio.tools, FASEB list |
is used by: NIF Data Federation is listed by: Debian is listed by: bio.tools is related to: AmiGO has parent organization: Simon Fraser University; British Columbia; Canada has parent organization: University of British Columbia; British Columbia; Canada |
Cystic Fibrosis Foundation Therapeutics Inc | PMID:18978025 | nif-0000-03369, r3d100012086, biotools:pseudomonas_genome_database | https://bio.tools/pseudomonas_genome_database, https://doi.org/10.17616/R3935H | SCR_006590 | Pseudomonas Genome Database - Improving Disease Treatment Through Genome Research | 2026-09-05 06:25:57 | 543 | |||||
|
MaizeGDB Resource Report Resource Website 1000+ mentions |
MaizeGDB (RRID:SCR_006600) | MaizeGDB | analysis service resource, data analysis service, data or information resource, data repository, database, organism-related portal, portal, production service resource, service resource, storage service resource, topical portal | Collection of data related to crop plant and model organism Zea mays. Used to synthesize, display, and provide access to maize genomics and genetics data, prioritizing mutant and phenotype data and tools, structural and genetic map sets, and gene models and to provide support services to the community of maize researchers. Data stored at MaizeGDB was inherited from the MaizeDB and ZmDB projects. Sequence data are from GenBank. Data are searchable by phenotype, traits, Pests, Gel Pattern, and Mutant Images. | zea mays, corn, model organism, genome, locus, metabolic pathway, genetics, genomics, sequence, gene product, function, literature reference, phenotype, trait, pest, gel pattern, mutant, blast, gene, image, corn, genotype-environment interaction, gene mapping, plant genome mapping, plant genome, gold standard, bio.tools, FASEB list |
is listed by: re3data.org is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: GenBank has parent organization: University of Maryland; Maryland; USA works with: Maize Database of Images and Genomes |
National Corn Growers Association ; NSF ; USDA/ARS ; USDA |
PMID:21624896 PMID:18769488 PMID:15888678 PMID:14681441 |
Free, Freely available, Acknowledgement requested, The community can contribute to this resource | OMICS_01655, biotools:MaizeDIG, nif-0000-03096, r3d100010795 | https://bio.tools/MaizeDIG, https://doi.org/10.17616/R3V32B | SCR_006600 | Maize Genetics and Genomics Database, MaizeGDB, MaizeGDB Locus | 2026-09-05 06:25:57 | 1047 | ||||
|
A plasmid Editor Resource Report Resource Website 100+ mentions |
A plasmid Editor (RRID:SCR_014266) | ApE | data analysis software, data processing software, sequence analysis software, software application, software resource, standalone software | Software tool for plasmid and sequence editing, annotating and drawing plasmid sequences. Used to view circular or linear maps of DNA sequences. Users can perform virtual digests whereby they select predefined DNA ladder, or specify their own, and visualize theoretical DNA fragments. Used to highlight restriction sites in editing window, accurately reflect Dam/Dcm blocking of enzyme sites, highlighting and drawing graphic maps using feature annotations from genbank and embl files, highlighting text using pre-defined and custom feature libraries, and directly BLASTing selected sequence at NCBI or Wormbase. Runs across Windows, OS X, and Linux/Unix. | Plasmid, editing, sequence, annotating, drawing, restriction, site, enzyme, map, DNA, fragment |
works with: GenBank works with: NCBI works with: WormBase |
Free, Available for download, Freely available | https://jorgensen.biology.utah.edu/wayned/ape/ | http://ape-a-plasmid-editor.wikispaces.com | SCR_014266 | A plasmid Editor | 2026-09-05 06:27:45 | 114 | ||||||
|
Princeton High Throughput Sequencing and Microarray Facility Resource Report Resource Website |
Princeton High Throughput Sequencing and Microarray Facility (RRID:SCR_012619) | Princeton High Throughput Sequencing and Microarray Facility, High Throughput Sequencing and Microarray Facility | access service resource, analysis service resource, core facility, data analysis service, production service resource, service resource | Core facility provides researchers with access to high-throughput sequencing technologies. The staff provide consultation on experimental design, library preparation, and data analysis. The Sequencing Core Facility works closely with Bioinformatics staff in the Center for Quantitative Biology to provide researchers with computing power and consulting services to analyze sequencing data. | sequence, microarray, data analysis, analysis, consulting, |
is listed by: ScienceExchange is related to: Princeton University Labs and Facilities has parent organization: Princeton University; New Jersey; USA |
Available to External User | SciEx_567 | SCR_012619 | High Throughput Sequencing, Microarray, Princeton University, Facility | 2026-09-05 06:27:25 | 0 | |||||||
|
SIFT Resource Report Resource Website 10000+ mentions |
SIFT (RRID:SCR_012813) | SIFT | analysis service resource, data access protocol, data analysis service, production service resource, service resource, software resource, source code, web service | Data analysis service to predict whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. SIFT can be applied to naturally occurring nonsynonymous polymorphisms and laboratory-induced missense mutations. (entry from Genetic Analysis Software) Web service is also available. | gene, genetic, genomic, amino acid, substitution, protein function, coding region, single nucleotide variant, coding indel, deletion, insertion, sequence, protein, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: SIFT 4G has parent organization: Genome Institute of Singapore; Singapore; Singapore has parent organization: J. Craig Venter Institute |
Agency for Science Technology and Research ; NIGMS GM29009 |
PMID:19561590 PMID:12824425 PMID:11337480 DOI:10.1038/nprot.2009.86 |
Non-commercial | biotools:sift, OMICS_00137, nlx_154618 | http://sift.jcvi.org/, https://bio.tools/sift, https://sources.debian.org/src/sift/ | http://sift.bii.a-star.edu.sg/SIFT.html | SCR_012813 | Sorting Intolerant From Tolerant | 2026-09-05 06:27:27 | 10996 | |||
|
Human Genome Project Information Resource Report Resource Website 50+ mentions |
Human Genome Project Information (RRID:SCR_013028) | data or information resource, funding resource, narrative resource, portal, slide, topical portal, training material, video resource | This resource gives information about the U.S. Human Genome Project, which was was a 13-year effort to to discover all the estimated 20,000-25,000 human genes and make them accessible for further biological study. The primary project goals were to: - identify all the approximately 20,000-25,000 genes in human DNA, - determine the sequences of the 3 billion chemical base pairs that make up human DNA, - store this information in databases, - improve tools for data analysis, - transfer related technologies to the private sector, and - address the ethical, legal, and social issues (ELSI) that may arise from the project. To help achieve these goals, researchers also studied the genetic makeup of several nonhuman organisms. These include the common human gut bacterium Escherichia coli, the fruit fly, and the laboratory mouse. These parallel studies helped to develop technology and interpret human gene function. Sponsors: The DOE Human Genome Program and the NIH National Human Genome Research Institute (NHGRI) together sponsored the U.S. Human Genome Project. | escherichia coli, fruit fly, function, gene, genome, genetic, bacterium, base pair, biological, dna, human, mouse, sequence, FASEB list |
has parent organization: National Institutes of Health has parent organization: United States Department of Energy |
nif-0000-10252 | SCR_013028 | HGP | 2026-09-05 06:27:31 | 59 | |||||||||
|
PolyPhen: Polymorphism Phenotyping Resource Report Resource Website 1000+ mentions |
PolyPhen: Polymorphism Phenotyping (RRID:SCR_013189) | PolyPhen, PolyPhen-2, POLYPHEN | data analysis software, data processing software, simulation software, software application, software resource | Software tool which predicts possible impact of amino acid substitution on structure and function of human protein using straightforward physical and comparative considerations. PolyPhen-2 is new development of PolyPhen tool for annotating coding nonsynonymous SNPs. | annotate, nonsynonymous, SNP, predict, coding, damaging, effect, missense, mutation, sequence, variant, phenotype, genetic, disease, exon, protein, coding, fraction, genome, bio.tools |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools is related to: OMICtools has parent organization: Harvard University; Cambridge; United States |
PMID:20354512 PMID:23315928 |
SCR_013200, OMICS_00136, nlx_154540, nif-0000-21329, biotools:polyphen, SCR_013238 | https://bio.tools/polyphen | http://www.bork.embl-heidelberg.de/PolyPhen/ | SCR_013189 | PolyPhen, POLYPHEN, PolyPhen-2, Polymorphism Phenotyping, Polymorphism Phenotyping v2 | 2026-09-05 06:27:33 | 4723 | |||||
|
DOLOP: A Database of Bacterial Lipoproteins Resource Report Resource Website 10+ mentions |
DOLOP: A Database of Bacterial Lipoproteins (RRID:SCR_013487) | data or information resource, data repository, database, service resource, storage service resource | DOLOP is an exclusive knowledge base for bacterial lipoproteins by processing information from 510 entries to provide a list of 199 distinct lipoproteins with relevant links to molecular details. Features include functional classification, predictive algorithm for query sequences, primary sequence analysis and lists of predicted lipoproteins from 43 completed bacterial genomes along with interactive information exchange facility. This website along will have additional information on the biosynthetic pathway, supplementary material and other related figures. DOLOP also contains information and links to molecular details for about 278 distinct lipoproteins and predicted lipoproteins from 234 completely sequenced bacterial genomes. Additionally, the website features a tool that applies a predictive algorithm to identify the presence or absence of the lipoprotein signal sequence in a user-given sequence. The experimentally verified lipoproteins have been classified into different functional classes and more importantly functional domain assignments using hidden Markov models from the SUPERFAMILY database that have been provided for the predicted lipoproteins. Other features include: primary sequence analysis, signal sequence analysis, and search facility and information exchange facility to allow researchers to exchange results on newly characterized lipoproteins. | figure, functional, algorithm, analysis, bacterial, biosynthetic, classification, genome, lipid, lipoprotein, modification, molecular, molecule, pathogenesis, predictive, primary, prokaryote, query, sequence, signal | has parent organization: University of Cambridge; Cambridge; United Kingdom | nif-0000-21124 | SCR_013487 | DOLOP | 2026-09-05 06:27:36 | 16 | |||||||||
|
MAFFT Resource Report Resource Website 10000+ mentions |
MAFFT (RRID:SCR_011811) | MAFFT | alignment software, data processing software, image analysis software, software application, software resource, software toolkit | Software package as multiple alignment program for amino acid or nucleotide sequences. Can align up to 500 sequences or maximum file size of 1 MB. First version of MAFFT used algorithm based on progressive alignment, in which sequences were clustered with help of Fast Fourier Transform. Subsequent versions have added other algorithms and modes of operation, including options for faster alignment of large numbers of sequences, higher accuracy alignments, alignment of non-coding RNA sequences, and addition of new sequences to existing alignments. | alignment, amino acid, nucleotide, sequence, DNA, sequence alignment, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
EMBL ; Ministry of Education ; Culture ; Sports ; Science and Technology of Japan |
PMID:12136088 PMID:17118958 PMID:16362903 PMID:15661851 PMID:18439255 PMID:23023983 DOI:10.1093/bib/bbn013 |
biotools:MAFFT, OMICS_00979 | https://www.ebi.ac.uk/Tools/msa/mafft/, https://www.genome.jp/tools-bin/mafft, https://myhits.isb-sib.ch/cgi-bin/mafft, https://bio.tools/MAFFT, https://sources.debian.org/src/mafft/ | SCR_011811 | Multiple Alignment using Fast Fourier Transform, MAFFT version 5, MAFFT version 7 | 2026-09-05 06:27:13 | 24687 | |||||
|
Wellcome Trust Sanger Institute; Hinxton; United Kingdom Resource Report Resource Website 500+ mentions |
Wellcome Trust Sanger Institute; Hinxton; United Kingdom (RRID:SCR_011784) | WTSI, Sanger | institution | Non profit research organization for genome sequences to advance understanding of biology of humans and pathogens in order to improve human health globally. Provides data which can be translated for diagnostics, treatments or therapies including over 100 finished genomes, which can be downloaded. Data are publicly available on limited basis, and provided more extensively upon request. | research, genome, sequence, human, health, project, global, data, treatment, therapy |
is listed by: re3data.org is affiliated with: Open Targets is related to: Clonalframe is related to: ClonalOrigin is related to: TraCeR is parent organization of: ILLUMINUS is parent organization of: ARNIE is parent organization of: Sequence Search and Alignment by Hashing Algorithm is parent organization of: Sequencing of Idd regions in the NOD mouse genome is parent organization of: CAROL is parent organization of: DINDEL is parent organization of: Wellcome Trust Case Control Consortium is parent organization of: OLORIN is parent organization of: Exomiser is parent organization of: COSMIC - Catalogue Of Somatic Mutations In Cancer is parent organization of: GeneDB is parent organization of: Breast Cancer Somatic Genetics Study is parent organization of: Artemis: Genome Browser and Annotation Tool is parent organization of: ACT: Artemis Comparison Tool is parent organization of: Alien hunter is parent organization of: Pfam is parent organization of: DNAPlotter is parent organization of: VAGrENT is parent organization of: SMALT is parent organization of: LookSeq is parent organization of: ZMP is parent organization of: Deciphering Developmental Disorders is parent organization of: Sanger Mouse Resources Portal is parent organization of: SpliceDB is parent organization of: DECIPHER is parent organization of: 1000 Genomes: A Deep Catalog of Human Genetic Variation is parent organization of: Genes to Cognition: Neuroscience Research Programme is parent organization of: MEROPS is parent organization of: Rfam is parent organization of: VEGA is parent organization of: Bacterial Genomes is parent organization of: Caenorhabditis Genome Sequencing Projects is parent organization of: D. rerio Blast Server is parent organization of: Fungi Sequencing Projects is parent organization of: PEER is parent organization of: Alfresco - FRont-End for Sequence COmparison is parent organization of: AutoCSA (Automatic Comparative Sequence Analysis) is parent organization of: AceDB is parent organization of: CnD is parent organization of: Genomics of Drug Sensitivity in Cancer is parent organization of: Zebrafish Genome Project is parent organization of: Tree families database is parent organization of: Ensembl is parent organization of: BamView is parent organization of: SVMerge is parent organization of: RetroSeq is parent organization of: Consensus CDS is parent organization of: WormBase is parent organization of: Belvu is parent organization of: Bio-tradis is parent organization of: Blixem is parent organization of: Dotter is parent organization of: Exonerate is parent organization of: Fastaq is parent organization of: Gubbins is parent organization of: CellPhoneDB is parent organization of: Ensembl Metazoa is parent organization of: Scmap is parent organization of: Scfind is parent organization of: Recognition of Errors in Assemblies using Paired Reads is parent organization of: SAMTOOLS is parent organization of: Cell Model Passports |
Wellcome Trust | ISNI: 0000 0004 0606 5382, nlx_91258, grid.10306.34, Wikidata: Q1142544 | https://ror.org/05cy4wa09 | SCR_011784 | Wellcome Trust Sanger Institute, Genome Research Limited, The Wellcome Sanger Institute, Sanger Institute, Wellcome Trust Sanger Institute Genome Research Limited | 2026-09-05 06:27:12 | 543 | ||||||
|
AdapterRemoval Resource Report Resource Website 500+ mentions |
AdapterRemoval (RRID:SCR_011834) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software program to remove residual adapter sequences from next generation sequencing reads. Used for cleaning of next-generation sequencing reads. AdapterRemoval v2 introduces improvements in throughput, through use of single instruction, multiple data (SIMD; SSE1 and SSE2) instructions and multi-threading support; handles datasets containing reads or read-pairs with different adapters or adapter pairs; provides simultaneous demultiplexing and adapter trimming; has ability to reconstruct adapter sequences from paired-end reads for poorly documented data sets; provides native gzip and bzip2 support. | cleaning of next-generation sequencing reads, remove residual adapter sequences, adapter, sequence, residual, next generation sequencing reads, |
is listed by: OMICtools is listed by: Debian |
Danish Council for Independent Research ; Danish National Research Foundation ; Lundbeck Foundation Grant ; Marie Curie International Outgoing Fellowship within the 7th European Community Framework Programme |
PMID:22748135 PMID:26868221 DOI:10.1186/s13104-016-1900-2 |
Free, Available for download, Freely available | OMICS_01081 | https://sources.debian.org/src/adapterremoval/ | http://code.google.com/p/adapterremoval/, https://github.com/slindgreen/AdapterRemoval, https://sources.debian.org/src/adapterremoval/ | SCR_011834 | AdapterRemoval v2 | 2026-09-05 06:27:13 | 773 | ||||
|
GMAP Resource Report Resource Website 500+ mentions |
GMAP (RRID:SCR_008992) | GMAP | alignment software, data processing software, image analysis software, software application, software resource, source code | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. A software program for mapping and aligning cDNA sequences to a genome. The program maps and aligns a single sequence with minimal startup time and memory requirements, and provides fast batch processing of large sequence sets. The program generates accurate gene structures, even in the presence of substantial polymorphisms and sequence errors, without using probabilistic splice site models. Methodology underlying the program includes a minimal sampling strategy for genomic mapping, oligomer chaining for approximate alignment, sandwich DP for splice site detection, and microexon identification with statistical significance testing. | mrna, est sequence, expressed sequence tag, sequence, cdna sequence, genome, cdna, bio.tools |
is used by: deFuse is listed by: Debian is listed by: bio.tools has parent organization: Genentech |
PMID:15728110 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_15072, biotools:gmap, nlx_152505 | https://bio.tools/gmap, https://sources.debian.org/src/gmap/ | SCR_008992 | 2026-09-05 06:26:31 | 599 | ||||||
|
CMAP Resource Report Resource Website 100+ mentions |
CMAP (RRID:SCR_009034) | CMap | data analysis software, data processing software, software application, software resource | Web-based tool that allows users to view comparisons of genetic and physical maps. The package also includes tools for curating map data. (entry from Genetic Analysis Software) | gene, genetic, genomic, perl, unix, solaris, freebsd, linux, sequence, FASEB list |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: SoftCite has parent organization: Generic Model Organism Database Project works with: Drug Gene Budger |
PMID:19648141 | GNU General Public License | nlx_153998, OMICS_00933 | https://sourceforge.net/projects/gmod/files/cmap/ | http://www.gmod.org/cmap/, http://gmod.org/wiki/Cmap | SCR_009034 | , GMOD Comparative Mapping (CMap) tool, Comparative Mapping tool, genetic and comparative maps | 2026-09-05 06:26:32 | 417 | ||||
|
eVOC Resource Report Resource Website 1+ mentions |
eVOC (RRID:SCR_010704) | eVOC | controlled vocabulary, data or information resource, ontology | THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone., documented September 6, 2016. Set of orthogonal controlled vocabularies that unifies gene expression data by facilitating a link between the genome sequence and expression phenotype information. The system associates labelled target cDNAs for microarray experiments, or cDNA libraries and their associated transcripts with controlled terms in a set of hierarchical vocabularies. eVOC consists of four orthogonal controlled vocabularies suitable for describing the domains of human gene expression data including Anatomical System, Cell Type, Pathology and Developmental Stage. The four core eVOC ontologies provide an appropriate set of detailed human terms that describe the sample source of human experimental material such as cDNA and SAGE libraries. These expression terms are linked to libraries and transcripts allowing the assessment of tissue expression profiles, differential gene expression levels and the physical distribution of expression across the genome. Analysis is currently possible using EST and SAGE data, with microarray data being incorporated. The eVOC data is increasingly being accepted as a standard for describing gene expression and eVOC ontologies are integrated with the Ensembl EnsMart database, the Alternate Transcript Diversity Project and the UniProt Knowledgebase. Several groups are currently working to provide shared development of this resource such that it is of maximum use in unifying transcript expression information. | mouse, mapping, cdna, development, microarray, expression, expressed sequence, anatomical system, cell type, developmental stage, experimental technique, microarray platform, pathology, pooling, tissue preparation, treatment, gene expression, genome sequence, expression phenotype, genome, sequence, phenotype, anatomical system, cell type, pathology, anatomy |
is related to: OBO is related to: Bgee: dataBase for Gene Expression Evolution has parent organization: University of the Western Cape; Bellville; South Africa |
South African National Research Foundation ; European Union ; Wellcome Trust ; South African Department of Arts Culture Science and Technology 32146 |
PMID:12799354 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_84448 | SCR_010704 | Expressed Sequence Annotation for Humans, eVOC (Expressed Sequence Annotation for Humans), eVOC Ontologies, eVOContology.org | 2026-09-05 06:26:45 | 4 | |||||
|
miRDeep Resource Report Resource Website 100+ mentions |
miRDeep (RRID:SCR_010829) | miRDeep2 | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool to identify known and novel miRNA genes in seven animal clades by analyzing sequenced RNAs. Used for discovering known and novel miRNAs from small RNA sequencing data. | miRNA, gene, animal, clade, analysis, sequence, RNA, data | is listed by: OMICtools | China Scholarship Council ; German Ministry of Education and Research ; Helmholtz Association ; Helmholtz-Alliance on Systems Biology ; Max Delbrück Centrum Systems Biology Network ; Senate of Berlin |
PMID:18392026 PMID:21911355 |
Free, Available for download, Freely available | OMICS_00373 | https://github.com/rajewsky-lab/mirdeep2 | SCR_010829 | 2026-09-05 06:26:48 | 182 | |||||
|
DIG IT - Database of Immunoglobulins and Integrated Tools Resource Report Resource Website 1+ mentions |
DIG IT - Database of Immunoglobulins and Integrated Tools (RRID:SCR_005924) | DIG IT, DIGIT | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | The Database of Immunoglobulins and Integrated Tools (DIG IT) is an integrated resource storing sequences of annotated immunoglobulin variable domains of NCBI database and enriched with tools for searching and analyzing them. It contains 145759 heavy chain sequences and 71404 light chain sequences (47168 kappa type and 24236 lambda type) with assigned canonical structures for the hypervariable loops and the data on the type of antigen as well as the pairing information of immunoglobulin heavy and light chains (9672 total pairs). The user can input the immunoglobulin variable domain sequence (amino acid or nucleotide) of interest (heavy chain variable domain sequence; light chain variable domain sequence or both) to retrieve the closest sequences (sorted according to e-value) with complete annotation. The user can also directly query the database by antigen type, canonical structure, germline family in accordance to the requirements. | sequence, immunoglobulin, variable domain, domain, heavy chain sequence, light chain sequence, antigen type, canonical structure, germline family, blast |
is related to: NCBI Nucleotide is related to: NCBI Protein Database has parent organization: Sapienza University of Rome; Rome; Italy |
IIT SEED ; King Abdullah University of Science and Technology KUK-I1-012-43; Ministry of Health Contract Onc_Ord 25/07 |
PMID:22080506 | The results obtained from the server shall be used for scientific purposes only, Excluding industrial or commercial purposes. Proper acknowledgement shall be made to the author of the server in publications resulting from the use of it. The results of the server shall not be made available to users outside the recipient''''s laboratory, Unless written consent is obtained. | nlx_149625 | http://www.biocomputing.it/ | http://www.biocomputing.it/digit4/ | SCR_005924 | Database of Immunoglobulins and Integrated Tools, DIG IT! Database of Immunoglobulins and Integrated Tools, DIG IT! Database of Immunoglobulins with Integrated Tools, Database of Immunoglobulins Integrated Tools, DIG IT! Integrated Ig Database, DIG IT - Database of Immunoglobulins Integrated Tools | 2026-09-05 06:25:44 | 1 | |||
|
PeptideMapper Resource Report Resource Website 1+ mentions |
PeptideMapper (RRID:SCR_005763) | PeptideMapper | data access protocol, software resource, web service | The PeptideMapper Web-Service provides alignments of peptide sequence alignments to proteins, mRNA, EST, and HTC sequences from Genbank, RefSeq, UniProt, IPI, VEGA, EMBL, and HInvDb. This mapping infrastructure is supported, in part, by the compressed peptide sequence database infrastructure (Edwards, 2007) which enables a fast, suffix-tree based mapping of peptide sequences to gene identifiers and a gene-focused detailed mapping of peptide sequences to source sequence evidence. The PeptideMapper Web-Service can be used interactively or as a web-service using either HTTP or SOAP requests. Results of HTTP requests can be returned in a variety of formats, including XML, JSON, CSV, TSV, or XLS, and in some cases, GFF or BED; results of SOAP requests are returned as SOAP responses. The PeptideMapper Web-Service maps at most 20 peptides with length between 5 and 30 amino-acids in each request. The number of alignments returned, per peptide, gene, and sequence type, is set to 10 by default. The default can be changed on the interactive alignments search form or by using the max web-service parameter. | peptide, sequence, protein, alignment, expressed sequence tag, mrna, est, htc, genbank, refseq, uniprot, ipi, vega, embl, hinvdb | has parent organization: Edwards Lab | NCI CA126189 | PMID:17437027 | nlx_149229 | SCR_005763 | PeptideMapper Web-Service, Peptide Mapper | 2026-09-05 06:25:41 | 4 |
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
