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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Pplacer Resource Report Resource Website 10+ mentions |
Pplacer (RRID:SCR_004737) | Pplacer | software resource | Software that places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis. | classification, phylogenetic classification |
is listed by: OMICtools has parent organization: Fred Hutchinson Cancer Center |
PMID:21034504 | OMICS_01462 | SCR_004737 | pplacer: phylogenetic placement and downstream analysis | 2025-04-19 06:42:34 | 29 | |||||||
|
TETRA Resource Report Resource Website 50+ mentions |
TETRA (RRID:SCR_004573) | TETRA | software resource | Standalone software programs that can be used to calculate how well tetranucleotide usage patterns in DNA sequences correlate. Such correlations can provide valuable hints on the relatedness of DNA sequences. | tetranucleotide, dna sequence |
is listed by: OMICtools has parent organization: Max Planck Institute for Marine Microbiology; Bremen; Germany |
PMID:15305919 PMID:15507136 |
OMICS_01474 | SCR_004573 | TETRA - Fragment assignment by intrinsic tetranucleotide frequencies | 2025-04-19 06:42:27 | 62 | |||||||
|
European Bioinformatics Institute Resource Report Resource Website 1000+ mentions |
European Bioinformatics Institute (RRID:SCR_004727) | EMBL-EBI | institution | Non-profit academic organization for research and services in bioinformatics. Provides freely available data from life science experiments, performs basic research in computational biology, and offers user training programme, manages databases of biological data including nucleic acid, protein sequences, and macromolecular structures. Part of EMBL. | organization, academic, bioinformatics, research, service, data, computational, biology, training, database, DNA, protein |
is used by: Blueprint Epigenome is listed by: re3data.org is related to: AgedBrainSYSBIO is related to: ProteomeXchange is related to: Open PHACTS is related to: RHEA is related to: TraCeR is related to: 3D-Beacons is related to: RNAcentral has parent organization: European Molecular Biology Laboratory is parent organization of: CoGenT++ is parent organization of: ENA Sequence Version Archive is parent organization of: Reaper - Demultiplexing trimming and filtering sequencing data is parent organization of: PeakAnalyzer is parent organization of: Tally is parent organization of: Clustal Omega is parent organization of: Biocatalogue - The Life Science Web Services Registry is parent organization of: Experimental Network for Functional Integration: A European Network of Excellence for Data Integration and Systems Biology is parent organization of: The Alternatve Splicing Database is parent organization of: BioModels is parent organization of: CHEBI is parent organization of: MAGE is parent organization of: Ensembl is parent organization of: MIAME is parent organization of: UniProt is parent organization of: Ligand-Gated Ion Channel Database is parent organization of: EBI Genomes is parent organization of: IMEx - The International Molecular Exchange Consortium is parent organization of: Toolbox at the European Bioinformatics Institute is parent organization of: Clustal W2 is parent organization of: ArrayExpress is parent organization of: IMGT/HLA is parent organization of: IntEnz- Integrated relational Enzyme database is parent organization of: IPD - Immuno Polymorphism Database is parent organization of: IPI is parent organization of: MicroArray and Gene Expression Markup Language is parent organization of: DaliLite Pairwise comparison of protein structures is parent organization of: Chemical Information Ontology is parent organization of: PANDIT : Protein and Associated Nucleotide Domains with Inferred Trees is parent organization of: Proteomics Identifications (PRIDE) is parent organization of: Software Ontology is parent organization of: FSSP - Families of Structurally Similar Proteins is parent organization of: Experimental Factor Ontology is parent organization of: Identifiers.org is parent organization of: HipSci is parent organization of: ProteomeXchange is parent organization of: Taxonomy is parent organization of: PDBe - Protein Data Bank in Europe is parent organization of: EBI Dbfetch is parent organization of: ProFunc is parent organization of: WSDbfetch (SOAP) is parent organization of: QuickGO is parent organization of: SAS - Sequence Annotated by Structure is parent organization of: UniProt DAS is parent organization of: UniParc at the EBI is parent organization of: Patent Abstracts is parent organization of: BioSample Database at EBI is parent organization of: Database of Genomic Variants Archive (DGVa) is parent organization of: European Genome phenome Archive is parent organization of: UniSave is parent organization of: ArchSchema is parent organization of: UniRef at the EBI is parent organization of: EBIMed is parent organization of: Kraken is parent organization of: SIMBioMS is parent organization of: Expression Profiler is parent organization of: Whatizit is parent organization of: InterProScan is parent organization of: VectorBase is parent organization of: DRCAT Resource Catalogue is parent organization of: FunTree is parent organization of: CREATE is parent organization of: BioMedBridges is parent organization of: PSICQUIC Registry is parent organization of: PDBsum is parent organization of: European Nucleotide Archive (ENA) is parent organization of: DrugPort is parent organization of: Ontology Lookup Service is parent organization of: EDAM Ontology is parent organization of: InterPro is parent organization of: MIRIAM Resources is parent organization of: EB-eye Search is parent organization of: SBO is parent organization of: Ensembl Genomes is parent organization of: NeuronVisio is parent organization of: IntAct is parent organization of: WSsas - Web Service for the SAS tool is parent organization of: Enzyme Structures Database is parent organization of: EMBOSS CpGPlot/CpGReport/Isochore is parent organization of: PaperMaker is parent organization of: CluSTr is parent organization of: Genome Reviews is parent organization of: GOA is parent organization of: Integr8 : Access to complete genomes and proteomes is parent organization of: IPD-ESTDAB- The European Searchable Tumour Line Database is parent organization of: IPD-HPA - Human Platelet Antigens is parent organization of: IPD-KIR - Killer-cell Immunoglobulin-like Receptors is parent organization of: IPD-MHC- Major Histocompatibility Complex is parent organization of: HilbertVis is parent organization of: Gene Expression Atlas is parent organization of: Parasite genome databases and genome research resources is parent organization of: Alternative Exon Database is parent organization of: AltExtron Database is parent organization of: Patent Data Resources is parent organization of: Pompep is parent organization of: Mouse finder is parent organization of: Gene Regulation Ontology is parent organization of: CiteXplore literature searching is parent organization of: MaxSprout is parent organization of: SRS is parent organization of: MicroCosm Targets is parent organization of: Kalign is parent organization of: MUSCLE is parent organization of: FASTA is parent organization of: WU-BLAST is parent organization of: Oases is parent organization of: HTS Mappers is parent organization of: CRAM is parent organization of: CSA - Catalytic Site Atlas is parent organization of: ArrayExpress (R) is parent organization of: WiggleTools is parent organization of: vsn is parent organization of: rlsim is parent organization of: ISA Infrastructure for Managing Experimental Metadata is parent organization of: BioMart Project is parent organization of: BioPerl is parent organization of: BioJS is parent organization of: EMDataResource.org is parent organization of: HTqPCR is parent organization of: Reactome is parent organization of: Europe PubMed Central is parent organization of: h5vc is parent organization of: LexGrid is parent organization of: Consensus CDS is parent organization of: 1000 Genomes: A Deep Catalog of Human Genetic Variation is parent organization of: OrChem is parent organization of: Orphanet Rare Disease Ontology is parent organization of: Reflect is parent organization of: BioLayout Express 3D is parent organization of: Virtual Fly Brain is parent organization of: GeneWise is parent organization of: PhenoMeNal is parent organization of: Ensembl Metazoa is parent organization of: Velvet |
EMBL member states ; European Union ; NIH ; Wellcome Trust ; UK Research Councils ; Industry Programme partners ; BBSRC |
grid.225360.0, Wikidata: Q1341845, ISNI: 0000 0000 9709 7726, nlx_72386 | https://ror.org/02catss52 | SCR_004727 | EBI, European Molecular Biology Laboratory - European Bioinformatics Institute | 2025-04-19 06:42:34 | 3674 | ||||||
|
National University of Malaysia; Selangor; Malaysia Resource Report Resource Website 1+ mentions |
National University of Malaysia; Selangor; Malaysia (RRID:SCR_004724) | UKM, NUM | university | UKM affirms integration of faith in Allah and constructive knowledge along with amalgamation of theory and practice as core fundamentals in advancement of knowledge, building of educated society and development of university. |
is parent organization of: ProLysED - Prokaryotic Lysis Enzymes Database is parent organization of: NRESTdb |
nlx_151798 | http://www.ukm.my/v3/ | SCR_004724 | Universiti Kebangsaan Malaysia, National University of Malaysia | 2025-04-19 06:42:33 | 2 | ||||||||
|
BioPig Resource Report Resource Website 1+ mentions |
BioPig (RRID:SCR_004636) | BioPig | software resource | Software providing a framework for genomic data analysis using Apache Pig and Hadoop. | mapreduce/hadoop, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Lawrence Berkeley National Laboratory |
PMID:24021384 | biotools:biopig, OMICS_01225 | https://bio.tools/biopig | SCR_004636 | 2025-04-19 06:42:30 | 2 | |||||||
|
Compugen Resource Report Resource Website 10+ mentions |
Compugen (RRID:SCR_004631) | CGEN | commercial organization | Drug discovery company providing pharma with protein and antibody therapeutics in the fields of Oncology and Immunology. | drug, diagnostic, protein therapeutics, target discovery, therapeutics, oncology, immunology, monoclonal antibody | Wikidata: Q5157220, grid.418916.3, nlx_63124, ISNI: 0000 0004 0506 4804 | https://ror.org/017vd4789 | SCR_004631 | Compugen Ltd | 2025-04-19 06:42:30 | 18 | ||||||||
|
Jackson Laboratory Resource Report Resource Website 10000+ mentions |
Jackson Laboratory (RRID:SCR_004633) | JAX | institution | An independent, nonprofit organization focused on mammalian genetics research to advance human health. Their mission is to discover the genetic basis for preventing, treating, and curing human disease, and to enable research for the global biomedical community. Jackson Laboratory breeds and manages colonies of mice as resources for other research institutions and laboratories, along with providing software and techniques. Jackson Lab also conducts genetic research and provides educational material for various educational levels. | genomic, disease, mouse model, human disease, biomaterial manufacture |
is listed by: One Mind Biospecimen Bank Listing is affiliated with: Integrative Human Microbiome Project is related to: ScienceExchange is related to: Federation of International Mouse Resources is related to: MGI strains is related to: One Mind Biospecimen Bank Listing is related to: Beta Cell Biology Consortium is related to: Mouse Mutagenesis Center for Developmental Defects is related to: GenomeMUSter is parent organization of: Mouse Models For Alzheimer's Disease Research is parent organization of: Type 1 Diabetes Resource is parent organization of: MouseCyc is parent organization of: Special Mouse Strains Resource is parent organization of: Gene Weaver is parent organization of: Mouse Phenome Database (MPD) is parent organization of: Jackson Laboratory Cytogenetic Models Resource is parent organization of: Parkinson's Disease Mouse Model Resource is parent organization of: Eye mutant resource - The Jackson Laboratory is parent organization of: Brainbow mouse resource at Jackson Labs is parent organization of: Short Course on the Genetics of Addiction is parent organization of: JAX Cre Repository is parent organization of: Donate a strain to The Jackson Laboratory Repository is parent organization of: Jackson Laboratory Neurobiology is parent organization of: QTL Archive is parent organization of: Mouse Genome Informatics: The Gene Ontology Project is parent organization of: Mouse Genome Informatics (MGI) is parent organization of: Mouse Tumor Biology Database is parent organization of: Gene Expression Database is parent organization of: The Jackson Laboratory Hearing Research Program is parent organization of: JAX Mice: Neural Tube Defects is parent organization of: JAX Neuroscience Mutagenesis Facility is parent organization of: Induced Mutant Resource is parent organization of: Mouse Mutant Resource is parent organization of: Mouse Genome Database is parent organization of: Mutant Mouse Resource and Research Center is parent organization of: eMouseAtlas is parent organization of: GBRS is parent organization of: Jackson Laboratory Scientific Instrument Services Core Facility provides: Knockout Mouse Project Repository |
Types 1 diabetes, Type 2 diabetes, Diabetes, Cardiovascular diseases, Metabolic disease, Cancer, Rare disease, Alzheimer's disease, Demantia | Available to the research community, Available to the educational community | nlx_63162, ISNI: 0000 0004 0374 0039, grid.249880.f, Crossref funder ID: 100005946 | https://ror.org/021sy4w91 | SCR_004633 | JAX Lab, Jackson Lab | 2025-04-19 06:42:30 | 14275 | |||||
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Nonpareil Resource Report Resource Website 50+ mentions |
Nonpareil (RRID:SCR_004629) | Nonpareil | software resource | Estimate average coverage and create Nonpareil curves for metagenomic datasets. | is listed by: OMICtools | PMID:24123672 | OMICS_01419 | SCR_004629 | 2025-04-19 06:42:29 | 68 | |||||||||
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Hema-Quebec Resource Report Resource Website 1+ mentions |
Hema-Quebec (RRID:SCR_004700) | nonprofit organization | Hema-Quebec''s mission is to efficiently provide adequate quantities of safe, optimal blood components, substitutes, human tissues and cord blood to meet the needs of all Quebecers; provide and develop expertise along with specialized and innovative services and products in the fields of transfusion medicine and human tissue transplantation. Hema-Quebec is driven by the commitment, support and recognition of its employees as well as the trust of its partners to remain the standard of quality and innovation with respect to the safe procurement of blood products, human tissues and stem cells. | is listed by: One Mind Biospecimen Bank Listing | Hema-Quebec Foundation | nlx_69414, ISNI: 0000 0001 2111 8890, grid.292497.3, Wikidata: Q3144906 | https://ror.org/008jvv944 | SCR_004700 | 2025-04-19 06:42:32 | 2 | |||||||||
|
PSP Association Resource Report Resource Website 1+ mentions |
PSP Association (RRID:SCR_004655) | PSP Association | nonprofit organization | The PSP Association is dedicated to the support of people with Progressive Supranuclear Palsy (PSP) and those who care for them. We also support those with the related, but rarer, disease Cortico Basal Degeneration (CBD). We fund research to better understand the possible causes of PSP and CBD, to find ways to achieve earlier and better diagnosis and to develop treatments that could potentially slow down, or even halt, the progression of these diseases. We support patients, families and carers through the services we offer on a UK-wide basis, through our Nurse Specialist helpline, our Local Support Groups, our publications (including the comprehensive Carers'' Information Pack) and our Annual Symposium for carers and therapists. We raise awareness of PSP and CBD on a local and national level and work in partnership with the relevant bodies and umbrella organisations in the UK to seek to make a positive difference to the lives of people with PSP and CBD. Registered charity numbers: England & Wales 1037087 / Scotland: SC041199. | progressive supranuclear palsy, cortico basal degeneration | grid.481174.f, Crossref funder ID: 501100008177, ISNI: 0000 0000 9330 6674, nlx_143855 | https://ror.org/05jmp0y43 | SCR_004655 | Progressive Supranuclear Palsy Association | 2025-04-19 06:42:31 | 2 | ||||||||
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AbundanceBin Resource Report Resource Website 1+ mentions |
AbundanceBin (RRID:SCR_004648) | AbundanceBin | software resource | An abundance-based software tool for binning metagenomic sequences, such that the reads classified in a bin belong to species of identical or very similar abundances. AbundanceBin also gives estimations of species abundances and their genome sizes -two important characteristic parameters for a microbial community. | metagenome, sequence |
is listed by: OMICtools has parent organization: Indiana University; Indiana; USA |
PMID:21385052 | Acknowledgement requested, Free, Public | OMICS_01471 | SCR_004648 | 2025-04-19 06:42:30 | 5 | |||||||
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Susan G. Komen for the Cure Resource Report Resource Website 10+ mentions |
Susan G. Komen for the Cure (RRID:SCR_004842) | Susan G. Komen | funding resource | Susan G. Komen for the Cure is the global leader of the breast cancer movement, having invested more than $1.9 billion since inception in 1982. As the world''s largest grassroots network of breast cancer survivors and activists, we''re working together to save lives, empower people, ensure quality care for all and energize science to find the cures. Thanks to events like the Susan G. Komen Race for the Cure and the Susan G. Komen 3-Day for the Cure, and generous contributions from our partners, sponsors and fellow supporters, we have become the largest source of nonprofit funds dedicated to the fight against breast cancer in the world. | is parent organization of: Susan G. Komen Tissue Bank | Wikidata: Q246898, grid.428834.1, nlx_82488, Crossref funder ID: 100000869, ISNI: 0000 0001 0241 5320 | https://ror.org/02nadbe75 | SCR_004842 | Susan G. Komen | 2025-04-19 06:42:40 | 24 | ||||||||
|
BMA Biomedicals Resource Report Resource Website 100+ mentions |
BMA Biomedicals (RRID:SCR_004833) | commercial organization | An Antibody supplier | nlx_152319 | SCR_004833 | 2025-04-19 06:42:40 | 174 | ||||||||||||
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Globus Medical, Inc. Resource Report Resource Website 1+ mentions |
Globus Medical, Inc. (RRID:SCR_004836) | Globus | commercial organization | A privately held spinal company that is driving significant technological advancements across a complete suite of spinal products. Founded in 2003, Globus'' single-minded focus on advancing spinal surgery has made it the fastest growing company in the history of orthopedics. Globus is driven to utilize superior engineering and technology to achieve pain free, active lives for all patients with spinal disorders. The ultimate goal at Globus is to deliver innovation by utilizing superior engineering and technology to help improve patients'' lives. This clinical inspiration is central to every endeavor we undertake. We have developed a Spine Innovation Engine to focus our efforts on delivering industry leading solutions to surgeons and their patients. Our Spine Innovation Engine has developed a portfolio that includes a comprehensive line of technologically-advanced spine products. To date we have released over 50 major products and have over 30 more in various stages of development. Clinical Studies are the foundation for advancing innovative spine care and Globus is committed to a robust investment into prospective and retrospective clinical trials to evaluate the safety and efficacy of our products. Globus is currently conducting several FDA-approved Investigational Device Exemption (IDE) clinical studies. | minimally invasive, motion preservation, cervical, intervertebral fusion, thoracolumbar, biomaterial, spinal cord, orthopedics | Spinal cord disorder | nlx_81975, ISNI: 0000 0004 0376 7450, grid.459811.0 | https://ror.org/04x4hjg39 | SCR_004836 | Globus Medical | 2025-04-19 06:42:40 | 2 | |||||||
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VariationHunter Resource Report Resource Website 10+ mentions |
VariationHunter (RRID:SCR_004865) | VariationHunter | software resource | A software tool for discovery of structural variation in one or more individuals simultaneously using high throughput technologies. | structural variation, genome, next-generation sequencing |
is listed by: OMICtools is related to: SPLITREAD has parent organization: Simon Fraser University; British Columbia; Canada has parent organization: SourceForge |
PMID:22048523 PMID:20529927 |
OMICS_00328 | SCR_004865 | VariationHunter-CommonLaw | 2025-04-19 06:42:40 | 12 | |||||||
|
Boston Biochem Resource Report Resource Website 100+ mentions |
Boston Biochem (RRID:SCR_004761) | commercial organization | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 17, 2021. An Antibody supplier. | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152321 | SCR_004761 | Boston Biochem Inc. | 2025-04-19 06:42:35 | 108 | ||||||||||
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University of Genoa; Genoa; Italy Resource Report Resource Website 1+ mentions |
University of Genoa; Genoa; Italy (RRID:SCR_004878) | university | UniGe, is one of the largest universities in Italy. It is located in the city of Genoa and regional Metropolitan City of Genoa, on the Italian Riviera in the Liguria region of northwestern Italy. The original university was founded in 1481. |
is related to: PharmaCog is parent organization of: EyesWeb |
grid.5606.5, ISNI:0000 0001 2151 3065, nlx_14821, Crossref funder ID:501100004702, Wikidata:Q593321 | https://ror.org/0107c5v14 | SCR_004878 | Universit� degli Studi di Genova, University of Genoa, Universita degli Studi di Genova, Universita di Genova, Universit� di Genova | 2025-04-19 06:42:40 | 2 | |||||||||
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XNAT Extras Resource Report Resource Website 1+ mentions |
XNAT Extras (RRID:SCR_004759) | XNAT Extras | software resource | User software contributions for XNAT - The Extensible Neuroimaging Archive Toolkit, http://www.xnat.org | computed tomography, database application, java, magnetic resonance, pet, spect, posix/unix-like, python, xnat pipeline |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: XNAT - The Extensible Neuroimaging Archive Toolkit |
PMID:25071542 | nlx_156023 | SCR_004759 | 2025-04-19 06:42:35 | 1 | ||||||||
|
Phymm and PhymmBL Resource Report Resource Website 10+ mentions |
Phymm and PhymmBL (RRID:SCR_004751) | Phymm, PhymmBL | software resource | Software for Phylogenetic Classification of Metagenomic Data with Interpolated Markov Models to taxonomically classify DNA sequences and accurately classify reads as short as 100 bp. PhymmBL, the hybrid classifier included in this distribution which combines analysis from both Phymm and BLAST, produces even higher accuracy. | metagenome, sequence, taxonomy, classification, phylogenetic classification, genome, short read |
is listed by: OMICtools has parent organization: University of Maryland; Maryland; USA |
NLM R01-LM006845 | PMID:19648916 PMID:21527926 |
Open-source license | OMICS_01461 | SCR_004751 | 2025-04-19 06:42:35 | 12 | ||||||
|
deStruct Resource Report Resource Website 1+ mentions |
deStruct (RRID:SCR_004747) | deStruct | software resource | A software tool for identifying structural variation in tumour genomes from whole genome illumina sequencing. | structural variation, genome, genomics |
is listed by: OMICtools has parent organization: Google Code |
Tumor, Cancer | Open unspecified license | OMICS_00314 | SCR_004747 | deStruct - Bioinformatics tool for identifying structural variation in tumour genomes | 2025-04-19 06:42:35 | 7 |
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