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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
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Database of Genomic Variants Archive (DGVa) Resource Report Resource Website 100+ mentions |
Database of Genomic Variants Archive (DGVa) (RRID:SCR_004896) | DGVa | data or information resource, data repository, database, service resource, storage service resource | Public repository that accepts direct submissions and provides archiving, accessioning and distribution of publicly available genomic structural variants, in all species. Variants are accessioned at the study and sample level, granting stable identifiers that can be used in publications. DGVa data is integrated with other EBI resources, including comprehensive EBI search and Ensembl genome browser. Exchanges data with companion database, dbVar, at National Center for Biotechnology Information.NOTE: since 2019 DGVa doesn't accept submissions. Please send the data for submission to European Variation Archive (EVA). | genome, dna, gene, expression, genetics, mapping, structural, variant, gold standard |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: re3data.org is related to: dbVar is related to: ISCA Consortium is related to: Database of Genomic Variants is related to: Ensembl Variation has parent organization: European Bioinformatics Institute |
PMID:23193291 PMID:24174537 |
Free, Freely available | nlx_86626, r3d100010814 | https://doi.org/10.17616/R3HK7Z | http://www.ebi.ac.uk/dgva/page.php, http://www.ebi.ac.uk/dgva/ | SCR_004896 | SciCrunch Registry | , DGVarchive, DGVa, Database of Genomic Variants Archive | 2026-11-07 11:55:40 | 211 | ||||
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DDBJ Omics Archive Resource Report Resource Website |
DDBJ Omics Archive (RRID:SCR_000597) | DOR | data or information resource, data repository, database, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 6,2023. Archival database of functional genomics data generated by microarray and highly parallel new generation sequencers. Data are exchanged between ArrayExpress at EBI and DOR in common MAGE-TAB format. Supports MIAME and MINSEQE-compliant data submissions. DOR issues accession numbers, E-DORD-n to experiment and A-DORD-n to array design. DOR exchanges public data with the EBI ArrayExpress in common MAGE-TAB format. Note: At present, DOR does not accept submissions. DDBJ will announce launch of DOR when it is ready. (2013/01/31) The data can be kept private until your paper is published. You can set the hold date for a maximum of 1 year and can change it. Registered records are released according to the Data Release Policy. | functional genomics, array, sequence |
is listed by: OMICtools is related to: ArrayExpress is related to: MIAME is related to: MINSEQE is related to: MAGE-TAB has parent organization: DNA DataBank of Japan (DDBJ) |
PMID:22110025 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01026 | http://trace.ddbj.nig.ac.jp/dor | SCR_000597 | SciCrunch Registry | Ddbj Omics aRchive | 2026-11-07 11:54:04 | 0 | |||||
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BEACON Resource Report Resource Website 1+ mentions |
BEACON (RRID:SCR_027484) | software repository, software resource, source code | Software application to perform Bayesian analysis on expression and gene dependency data across different cell lineages. Integrates expression as the dependent variable and gene dependency data as the independent variable. Used to identify cancer gene targets by jointly analyzing global transcriptomic and proteomic profiles with genetic dependency data of cancer cell lines across tissue lineages. | analyzing global transcriptomic, proteomic profiles, genetic dependency data, cancer cell lines, | PMID:39484404 | Free, Available for download, Freely available | SCR_027484 | SciCrunch Registry | 2026-11-07 12:06:59 | 2 | ||||||||||
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Stem Cell Commons Resource Report Resource Website 1+ mentions |
Stem Cell Commons (RRID:SCR_004415) | Stem Cell Commons | analysis service resource, data or information resource, data repository, data set, database, production service resource, service resource, software resource, source code, storage service resource | Open source environment for sharing, processing and analyzing stem cell data bringing together stem cell data sets with tools for curation, dissemination and analysis. Standardization of the analytical approaches will enable researchers to directly compare and integrate their results with experiments and disease models in the Commons. Key features of the Stem Cell Commons * Contains stem cell related experiments * Includes microarray and Next-Generation Sequencing (NGS) data from human, mouse, rat and zebrafish * Data from multiple cell types and disease models * Carefully curated experimental metadata using controlled vocabularies * Export in the Investigation-Study-Assay tabular format (ISA-Tab) that is used by over 30 organizations worldwide * A community oriented resource with public data sets and freely available code in public code repositories such as GitHub Currently in development * Development of Refinery, a novel analysis platform that links Commons data to the Galaxy analytical engine * ChIP-seq analysis pipeline (additional pipelines in development) * Integration of experimental metadata and data files with Galaxy to guide users to choose workflows, parameters, and data sources Stem Cell Commons is based on open source software and is available for download and development. | therapeutic target, blood, stem cell, self-renewal, embryonic stem cell, hematopoietic stem cell, leukemia stem cell, gene, protein, phenotype, therapeutic, annotate, share, analyze, data sharing, statistics, visualize, analyze, microarray, next-generation sequencing, statistics, transcription profiling, genome, genome browser, disease model |
is related to: Galaxy is related to: ISA Infrastructure for Managing Experimental Metadata has parent organization: Harvard Stem Cell Institute |
Normal, Acute Myelogenous Leukemia, Glioblastoma, Primitive Neuroectodermal Tumor, Etc. | PMID:24303302 | Open unspecified license | nlx_42085 | http://bloodprogram.hsci.harvard.edu/ | SCR_004415 | SciCrunch Registry | HSCI Blood Genomics, Harvard Stem Cell Institute Blood Genomics, Harvard Stem Cell Institute Blood Program, HSCI Blood Program | 2026-11-07 11:55:20 | 2 | ||||
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NIDDK Inflammatory Bowel Disease Genetics Consortium Resource Report Resource Website 1+ mentions |
NIDDK Inflammatory Bowel Disease Genetics Consortium (RRID:SCR_001461) | IBDGC, NIDDKIBDGC | biomaterial supply resource, cell repository, material resource | Repository of biospecimen and phenotype data collected from Crohn's disease and ulcerative colitis cases and controls recruited at six sites throughout North America that are available to the scientific community. Phenotyping is performed using a standardized protocol, and lymphoblastoid cell lines are established for each subject. Phenotype data for each subject are collected by the Consortium's Data Coordinating Center (DCC), and phenotype data for all subjects with DNA samples are available. The resulting DNA samples have already been utilized by the Consortium to complete various association studies, including genome-wide association studies using dense genotyping arrays. Researchers can obtain DNA samples and phenotype, genotype, and pedigree data through the Data Repository. GWAS data must be requested through dbGAP. The IBDGC is involved with independent genetic research studies and actively works with members of the IBD and genetic communities on collaborative projects. They are also members of the International IBD Genetics Consortium. Phenotype Tools: The Consortium Phenotype Committee, led by Dr. Hillary Steinhart designed and validated paper forms to collect extensive phenotype data on Crohn's Disease and ulcerative colitis. Consortium phenotype tools are available for use by non-Consortium members. | dna, cell line, serum, lymphocyte, lymphoblastoid cell line, gene, loci, genetic analysis, blood, phenotype, genome-wide association study, genotype, pedigree, metadata standard, genotyping array |
uses: NCBI database of Genotypes and Phenotypes (dbGap) is listed by: One Mind Biospecimen Bank Listing is listed by: NIDDK Information Network (dkNET) has parent organization: Yale School of Medicine; Connecticut; USA |
Inflammatory Bowel Disease, Crohn's disease, Ulcerative colitis, Control, Family member | NIDDK U01 DK062429 | Free, Freely Available | nlx_152706 | http://medicine.yale.edu/intmed/ibdgc/ | SCR_001461 | SciCrunch Registry | IBD Genetics Consortium, NIDDKIBD Genetics Consortium, Inflammatory Bowel Disease Genetic Consortium | 2026-11-07 12:01:23 | 3 | ||||
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SCAR Antarctic Biodiversity Portal Resource Report Resource Website 1+ mentions |
SCAR Antarctic Biodiversity Portal (RRID:SCR_023136) | data repository, service resource, storage service resource | International effort that seeks to increase our knowledge and understanding of Antarctic and Southern Ocean biodiversity.It is a community of researchers, data custodians and developers from around the world that supports the mobilisation publication, retrieval and analysis of Antarctic and Southern Ocean biodiversity data in a free and open manner in line with the Antarctic treaty and the FAIR data Principles (Finable, Accessible, Interoperable, Reusable). The SCAR Antarctic biodiversity Portal has a number of portals dedicated to specific types of data and information on Antarctic and Southern Ocean Biodiversity.We aim to create an information ecosystem of various data bases, data systems, web services tools etc that can be used by anyone with an interest in Antarctic and Southern Ocean biodiversity.Biodiversity.aq is an international initiative of the Scientific Committee on Antarctic Research (SCAR). It finds it roots in the Census of Antarctic Marine Life and started in 2005. The central facilities are hosted by the Royal Belgian Institute for Natural sciences (RBINS, www.naturalsciences.be) and the Belgian Biodiversity Platform (BBPf, www.biodiversity.be).The SCAR Antarctic Biodiversity Portal is the regional thematic node of the Ocean Biodiversity Information System (OBIS, www.obis.org), the Global Biodiversity Information Facility (GBIF, www.gbif.org) and works closely together with the Southern Ocean Observation System (SOOS, www.soos.aq). | is listed by: DataCite | Free, Freely available | DOI:10.48361 | https://doi.org/10.48361, https://dx.doi.org/10.48361 | SCR_023136 | SciCrunch Registry | SCAR Antarctic Biodiversity Portal | 2026-11-07 12:01:03 | 9 | ||||||||
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Kidney and Urinary Pathway Knowledge Base Resource Report Resource Website 1+ mentions |
Kidney and Urinary Pathway Knowledge Base (RRID:SCR_001746) | KUPKB | analysis service resource, data analysis service, data or information resource, data repository, data set, production service resource, service resource, storage service resource | A collection of omics datasets (mRNA, proteins and miRNA) that have been extracted from PubMed and other related renal databases, all related to kidney physiology and pathology giving KUP biologists the means to ask queries across many resources in order to aggregate knowledge that is necessary for answering biological questions. Some microarray raw datasets have also been downloaded from the Gene Expression Omnibus and analyzed by the open-source software GeneArmada. The Semantic Web technologies, together with the background knowledge from the domain's ontologies, allows both rapid conversion and integration of this knowledge base. SPARQL endpoint http://sparql.kupkb.org/sparql The KUPKB Network Explorer will help you visualize the relationships among molecules stored in the KUPKB. A simple spreadsheet template is available for users to submit data to the KUPKB. It aims to capture a minimal amount of information about the experiment and the observations made. | kidney, urinary, urine, pathway, molecule, visualizer, gene, protein, mirna, metabolite, mrna, microarray, ortholog, rdf, renal cell, anatomy, animal model, disease, sparql, proteomics, ontology, biomarker, gene expression, physiology, pathology |
is related to: NIDDK Information Network (dkNET) is related to: Gene Expression Omnibus is related to: Gene Ontology is related to: KEGG has parent organization: University of Manchester; Manchester; United Kingdom has parent organization: National Institute of Health and Medical Research; Rennes; France |
Kidney disease | European Union ; FP7 ; ICT-2007.4.4 e-LICO project |
PMID:21624162 | THIS RESOURCE IS NO LONGER IN SERVICE. | nlx_154134 | http://www.e-lico.eu/kupkb | SCR_001746 | SciCrunch Registry | Kidney & Urinary Pathway Knowledge Base | 2026-11-07 11:54:39 | 2 | |||
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CBFBIRN Resource Report Resource Website 1+ mentions |
CBFBIRN (RRID:SCR_009543) | CBFBIRN | data or information resource, data repository, data set, service resource, storage service resource |
THIS RESOURCE IS NO LONGER IN SERVICE. Documented August 23, 2017. A web based central repository for individual and group analysis of Arterial Spin Labeling (ASL) data sets and ASL pulse sequences developed at CMFRI UCSD for MRI researchers. This resource currently hosts more 1300 ASL data sets from 22 projects and consists of mainly two main tools 1) The Cerebral Blood Flow Database and Analysis Pipeline (CBFDAP) is a web enabled data and workflow management system extended from the HID codebase on NITRC specialized for Arterial Spin Labeling data management and analysis (including group analysis) in a centralized manner. 2) Pulse Sequence Distribution System (PSDS) for managing dissamination of ASL pulse sequences developed at the UCSD CFMRI. This resource also includes web and video tutorials for end users. |
java, javascript, matlab, magnetic resonance, os independent, web environment, arterial spin labeling, mri |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Cerebral Blood Flow Database and Analysis Pipeline has parent organization: University of California at San Diego; California; USA |
NIH | PMID:24151465 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155722 | http://www.nitrc.org/projects/cbfbirn | SCR_009543 | SciCrunch Registry | Cerebral Blood Flow Biomedical Informatics Research Network | 2026-11-07 11:56:52 | 3 | ||||
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IMEx - The International Molecular Exchange Consortium Resource Report Resource Website 100+ mentions |
IMEx - The International Molecular Exchange Consortium (RRID:SCR_002805) | IMEx | community building portal, consortium, data or information resource, data repository, database, organization portal, portal, service resource, storage service resource | Interaction database from international collaboration between major public interaction data providers who share curation effort and develop set of curation rules when capturing data from both directly deposited interaction data or from publications in peer reviewed journals. Performs complete curation of all protein-protein interactions experimentally demonstrated within publication and makes them available in single search interface on common website. Provides data in standards compliant download formats. IMEx partners produce their own separate resources, which range from all encompassing molecular interaction databases, such as are maintained by IntAct, MINT and DIP, organism-centric resources such as BioGrid or MPIDB or biological domain centric, such as MatrixDB. They have committed to making records available, via PSICQUIC webservice, which have been curated to IMEx rules and are available to users as single, non-redundant set of curated publications which can be searched at the IMEx website. Data is made available in standards-compliant tab-deliminated and XML formats, enabling to visualize data using wide range of tools. Consortium is open to participation of additional partners and encourages deposition of data, prior to publication, and will supply unique accession numbers which may be referenced within final article. Submitters may send their data directly to any of member databases using variety of formats, but should conform to guidelines as to minimum information required to describe data. | protein-protein interaction, nonredundant, protein interaction, interaction, proteomics, metadata standard, short course, molecular interaction, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is affiliated with: MINT is related to: MatrixDB is related to: MPIDB is related to: Database of Interacting Proteins (DIP) is related to: Database of Interacting Proteins (DIP) is related to: InnateDB is related to: IntAct is related to: Interaction Reference Index is related to: MPIDB is related to: UniProt is related to: InnateDB is related to: MatrixDB is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: I2D is related to: Molecular Connections NetPro is related to: SIB Swiss Institute of Bioinformatics is related to: IntAct is related to: PSI-MI is related to: PSICQUIC Registry is related to: mentha is related to: Bioconductor has parent organization: European Bioinformatics Institute works with: CellPhoneDB works with: Cytoscape works with: IntAct works with: MINT works with: MPact: Representation of Interaction Data at MIPS works with: Molecular Connections NetPro works with: Biological General Repository for Interaction Datasets (BioGRID) works with: InnateDB works with: BIND |
European Union | PMID:22453911 PMID:17893861 |
Free, Freely available, Available for download | nif-0000-00447, OMICS_01545, r3d100010669, biotools:imex | http://imex.sourceforge.net/, https://bio.tools/imex, https://doi.org/10.17616/R3090W | SCR_002805 | SciCrunch Registry | The International Molecular Exchange Consortium, International Molecular Exchange Consortium | 2026-11-07 11:54:59 | 161 | ||||
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MethDB Resource Report Resource Website 10+ mentions |
MethDB (RRID:SCR_003108) | MethDB | data or information resource, data repository, database, service resource, storage service resource | Database that provides a resource to store DNA methylation data and to make these data readily available to the public. Future development of the database will focus on environmental effects on DNA methylation. No restriction applies on the type of data, i.e. as well as global estimations (e.g. HPLC) as data from high resolution analysis (i.e. sequencing) can be stored. As much background information as possible should be provided by the users. This includes the origin of the sample, phenotype, expression of the related gene, etc.. | methylation |
is listed by: OMICtools has parent organization: University of Perpignan Via Domitia; Perpignan; France has parent organization: French National Center for Scientific Research |
PMID:11125109 PMID:17965614 PMID:12163707 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03119, OMICS_01840 | http://www.methdb.net/ | SCR_003108 | SciCrunch Registry | DNA Methylation Database, MethDB - the database for DNA methylation and environmental epigenetic effects | 2026-11-07 11:55:08 | 15 | |||||
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Magnetics Information Consortium Resource Report Resource Website 10+ mentions |
Magnetics Information Consortium (RRID:SCR_007098) | MagIC | data or information resource, data repository, database, service resource, software resource, storage service resource | Databases that accept and provide access to paleomagnetic and rock magnetic data. The paleomagnetic data range from individual measurements to specimen, sample or site level results, including a wide variety of derived parameters or associated rock magnetic measurements. The rock magnetic database includes data collected during rock magnetic experiments on remanence, anisotropy, hysteresis and susceptibility. The MagIC Console Software provides an effective environment in Microsoft Excel where users can collate and prepare their paleomagentic and rock magnetic data for uploading in the Online MagIC Database. | paleomagnetism, rock, magnetic, paleomagnetic, geomagnetic, rock magnetic |
is listed by: CINERGI has parent organization: San Diego Supercomputer Center |
NSF EAR 0202996; NSF EAR-IF 0318672-0744107-0744108 |
Non-commercial, For scientific or educational purposes, Acknowledgement required, Copyrighted, The community can contribute to this resource | nlx_154712, SciRes_000151, r3d100011910 | https://doi.org/10.17616/R3NM0W | SCR_007098 | SciCrunch Registry | Magnetics Information Consortium (MagIC), MagIC Portal, MagIC database | 2026-11-07 11:56:08 | 34 | |||||
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Gene Weaver Resource Report Resource Website 10+ mentions |
Gene Weaver (RRID:SCR_003009) | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource | Freely accessible phenotype-centered database with integrated analysis and visualization tools. It combines diverse data sets from multiple species and experiment types, and allows data sharing across collaborative groups or to public users. It was conceived of as a tool for the integration of biological functions based on the molecular processes that subserved them. From these data, an empirically derived ontology may one day be inferred. Users have found the system valuable for a wide range of applications in the arena of functional genomic data integration. | phenotype, microarray, gene, genome, functional genomics, process, pathway, function, gene set, genomic data integration, analysis, visualization |
is used by: NIF Data Federation is used by: Integrated Datasets is listed by: OMICtools is related to: Integrated Manually Extracted Annotation has parent organization: Jackson Laboratory |
Integrative Neuroscience Initiative on Alcoholism ; NIAAA R01 AA18776; NIAAA U01 AA13499; NIAAA U24 AA13513 |
PMID:22080549 PMID:19733230 |
Free, Freely available | r3d100012464, OMICS_02232, nif-0000-00517 | http://ontologicaldiscovery.org/, https://doi.org/10.17616/R3248T | SCR_003009 | SciCrunch Registry | GeneWeaver, GeneWeaver - A system for the integration of functional genomics experiments, Ontological Discovery Environment, GeneWeaver.org | 2026-11-07 12:00:45 | 39 | |||||
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Animal Genome Size Database Resource Report Resource Website 100+ mentions |
Animal Genome Size Database (RRID:SCR_007551) | Genomesize | catalog, data or information resource, data repository, database, service resource, storage service resource | Comprehensive catalogue of animal genome size data. Haploid DNA contents (C-values, in picograms) are available for 4972 species (3231 vertebrates and 1741 non-vertebrates) based on 6518 records from 669 published sources. Data may be submitted directly to the database or reprints and notifications of new papers may be sent to database curation staff. | genome size, haploid dna, non-vertebrate, vertebrate, genome structure, comparative biodiversity, sequencing, genome, genomic, FASEB list | has parent organization: University of Guelph; Ontario; Canada | Natural Sciences and Engineering Research Council of Canada | PMID:17090588 | Data taken from the database must not be reproduced in published lists, Online databases, Or other such formats, Nor redistributed without permission. The information is provided solely for personal and academic use., Please cite, The community can contribute to this resource | nif-0000-02548, r3d100012517 | https://doi.org/10.17616/R3R782, https://doi.org/10.17616/R3R782 | SCR_007551 | SciCrunch Registry | 2026-11-07 11:56:26 | 190 | |||||
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Metabolomics Workbench Metabolite Database Resource Report Resource Website |
Metabolomics Workbench Metabolite Database (RRID:SCR_014633) | data or information resource, database | A database which contains structures and annotations of biologically relevant metabolites from public repositories such as LIPID MAPS, ChEBI, HMDB, PubChem, and KEGG. Users can search for molecular structure based on substructure, text, or mass. | database, metabolomics, metabolite, structure, annotation | has parent organization: Metabolomics Workbench | Public | SCR_014633 | SciCrunch Registry | UCSD Metabolomics Workbench Metabolite Database, Metabolomics Workbench Database | 2026-11-07 12:03:14 | 0 | |||||||||
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GeoStrat Resource Report Resource Website |
GeoStrat (RRID:SCR_009428) | GeoStrat | data or information resource, data repository, database, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 29,2019. Sedimentary geologic and biostratigraphic data. | sediment, geology, biostratigraphy | is listed by: CINERGI | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154709 | SCR_009428 | SciCrunch Registry | 2026-11-07 11:56:42 | 0 | ||||||||
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Organelle DB Resource Report Resource Website 1+ mentions |
Organelle DB (RRID:SCR_007837) | Organelle DB | d spatial image, data or information resource, data repository, database, image collection, service resource, storage service resource | Database of organelle proteins, and subcellular structures / complexes from compiled protein localization data from organisms spanning the eukaryotic kingdom. All data may be downloaded as a tab-delimited text file and new localization data (and localization images, etc) for any organism relevant to the data sets currently contained in Organelle DB is welcomed. The data sets in Organelle DB encompass 138 organisms with emphasis on the major model systems: S. cerevisiae, A. thaliana, D. melanogaster, C. elegans, M. musculus, and human proteins as well. In particular, Organelle DB is a central repository of yeast protein localization data, incorporating results from both previous and current (ongoing) large-scale studies of protein localization in Saccharomyces cerevisiae. In addition, we have manually curated several recent subcellular proteomic studies for incorporation in Organelle DB. In total, Organelle DB is a singular resource consolidating our knowledge of the protein composition of eukaryotic organelles and subcellular structures. When available, we have included terms from the Gene Ontologies: the cellular component, molecular function, and biological process fields are discussed more fully in GO. Additionally, when available, we have included fluorescent micrographs (principally of yeast cells) visualizing the described protein localization. Organelle View is a visualization tool for yeast protein localization. It is a visually engaging way for high school and undergraduate students to learn about genetics or for visually-inclined researchers to explore Organelle DB. By revealing the data through a colorful, dimensional model, we believe that different kinds of information will come to light. | gene, fly, vertebrate, human, mouse, plant, worm, yeast, protein, k-12, organelle, protein localization, function, subcellular structure, protein complex, sequence, annotation, micrograph, visualization, data analysis service |
is related to: Gene Ontology has parent organization: University of Michigan; Ann Arbor; USA |
American Cancer Society Research Scholar Grant RSG-06-179-01-MBC; March of Dimes Basil O'Connor Starter Scholar Research award 5-FY05-1224; NSF DBI-0543017 |
PMID:17130152 PMID:15608270 |
Free, Acknowledgement requested | nif-0000-03226 | SCR_007837 | SciCrunch Registry | Organelle DB: A Database of Organelles and Protein Complexes | 2026-11-07 11:56:27 | 7 | |||||
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Expression Database in 4D Resource Report Resource Website 1+ mentions |
Expression Database in 4D (RRID:SCR_007066) | 4DXpress | data or information resource, data repository, database, service resource, storage service resource | This database provides a platform to query and compare gene expression data during the development of the major model animals (zebrafish, drosophila, medaka, mouse). The name 4DXpress stands for expression database in 4D. The 4D (four dimensions) of 4DXpress can be interpreted either as: 3 spatial dimensions plus time, or as 1. species 2. gene 3. developmental stage 4. anatomical structure. The major focus of this database lies in cross species comparison. The high resolution expression data was acquired through whole mount in situ hybridsation-, antibody- or transgenic experiments. Data was integrated from several species specific expression pattern databases, such as ZFIN, BDGP, GXD, MEPD as well as directly submitted by researchers of the participating groups at EMBL. The 4DXpress database is a project within the Centre for Computational Biology at EMBL. It is developed by Yannick Haudry, Thorsten Henrich and Ivica Letunic and coordinated by Thorsten Henrich. Hugo Berube is developing the 4D ArrayExpress Data Warehouse at EBI for integrating in situ data with microarray data. | genes, anatomical structures, developmental stage, microarray data, species, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: European Molecular Biology Laboratory |
European Molecular Biology Laboratory; Heidelberg; Germany | PMID:17916571 | nif-0000-02524, biotools:4dxpress | https://bio.tools/4dxpress | SCR_007066 | SciCrunch Registry | 4DXpress Database | 2026-11-07 11:56:07 | 1 | |||||
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dbVar Resource Report Resource Website 100+ mentions |
dbVar (RRID:SCR_003219) | dbVar | data or information resource, data repository, database, service resource, storage service resource | Structural variation database designed to store data on variant DNA > / = 1 bp in size from all organisms. Associations of defined variants with phenotype information is also provided. Users can browse data containing number of variant cells from each study, and filter studies by organism, study type, method and genomic variant. Organisms include human, mouse, cattle and several additional animals. | structure, variation, structural variation, genetics, insertion, deletion, copy number variant, inversion, translocation, genomic imbalance, genotype, gene expression, dna, genomics, phenotype, genetic code |
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: re3data.org is related to: Database of Genomic Variants Archive (DGVa) is related to: Database of Genomic Variants has parent organization: NCBI |
PMID:23193291 | Free, Freely available | nlx_157217, r3d100010758 | https://doi.org/10.17616/R3V610 | SCR_003219 | SciCrunch Registry | dbVar, Database of Genomic Structural Variation, NCBI dbVar | 2026-11-07 11:54:57 | 198 | |||||
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bio.tools Resource Report Resource Website 10+ mentions |
bio.tools (RRID:SCR_014695) | catalog, data or information resource, database, software repository, software resource | Community registry of software tools and data resources for life sciences. Tools and data services registry as community effort to document bioinformatics resources. Registry of software and databases, facilitating researchers from across spectrum of biological and biomedical science. When adding tools to registry, information including URL, contact information, resource function, field its relevant in, and its primary publication are required. Development is supported by ELIXIR - the European Infrastructure for Biological Information. | Registry, software registry, biological tool, data services registry, services discovery portal, bio.tools |
lists: FACS lists: Fusion Analyser lists: AffyRNADegradation lists: GUARDD lists: GEOquery lists: RNAcontext lists: Patchwork lists: SODOCK lists: MIMOSA lists: GraBCas lists: SNAVI lists: GENIE3 lists: Megraft lists: MODENT - A Tool For Reconstructing Gene Regulatory Networks lists: PeptideProphet lists: Quant lists: VARiD lists: ProteinProphet lists: Flicker lists: ARACHNE lists: Micro-Analyzer lists: riboPicker lists: dbSTS lists: POPBAM lists: flowPeaks lists: cn.FARMS lists: Sequence Search and Alignment by Hashing Algorithm lists: SAMBLASTER lists: Pindel lists: Mfuzz lists: TAPyR lists: ContEst lists: PGS lists: PEPPER lists: FPSAC lists: FlipFlop lists: ProGlycProt lists: MuTect lists: TriageTools lists: BLASR lists: DSRC lists: SRMA lists: Bowtie lists: StringTie lists: PhenoFam lists: SOAP lists: SplitSeek lists: MUSCLE lists: SplicePlot lists: Illuminator lists: GimmeMotifs lists: Skylign lists: BreakSeq lists: Barrnap lists: SLOPE lists: CUDA-EC lists: QualiMap lists: massiR lists: OmicsOffice for NGS SeqSolve lists: QUAST lists: GenomicTools lists: NGSUtils lists: TileQC lists: Sequedex lists: PARalyzer lists: BFCounter lists: TALLYMER lists: SNPchip lists: VAAL lists: ProbRNA lists: ADMIXTURE lists: SABER lists: piCALL lists: CYCLE lists: limmaGUI lists: DEXUS lists: KAnalyze lists: BeadDataPackR lists: wateRmelon lists: NGSrich lists: OLIN lists: fRMA lists: MACAT lists: affylmGUI lists: DictyOGlyc lists: GlyProt lists: CisGenome lists: ToppCluster lists: AnimalTFDB lists: oneChannelGUI lists: YinOYang lists: Chilibot: Gene and Protein relationships from MEDLINE lists: asSeq lists: FARMS lists: GERMLINE lists: unifiedWMWqPCR lists: HAPLOPAINTER lists: Biocatalogue - The Life Science Web Services Registry lists: HOMOZYGOSITYMAPPER lists: MetaBase lists: PyLOH lists: InterMine lists: myExperiment lists: pRESTO lists: TANGO lists: Prediction of Amyloid Structure Aggregation lists: PhosphoSitePlus: Protein Modification Site lists: CCAT lists: BREAKDANCER lists: FACTA+. lists: PEDIGRAPH lists: CQN lists: CanSNPer lists: SamSPECTRAL lists: TEMP lists: MEME Suite - Motif-based sequence analysis tools lists: SNPAAMapper lists: Pecan lists: InteroPorc lists: AffyPipe lists: ADaCGH2 lists: DINDEL lists: ASPGD lists: Candida Genome Database lists: BISC lists: PurBayes lists: SNVer lists: Cake lists: S-MART lists: SHORTY lists: Pathway Commons lists: TcoF lists: BEETL-fastq lists: SBARS lists: cpnDB: A Chaperonin Database lists: cisRED: cis-regulatory element lists: FlyFactorSurvey lists: pymzML lists: EchoBASE lists: Blood Group Antigen Gene Mutation Database lists: WebGeSTer DB lists: RUbioSeq lists: COSMIC - Catalogue Of Somatic Mutations In Cancer lists: MethylAid lists: ExomeDepth lists: ZOOM lists: Iterative Signature Algorithm lists: ShotGun lists: Pathview lists: T3DB lists: Autophagy Database lists: rBiopaxParser lists: QualitySNPng lists: CAMERA - Collection of annotation related methods for mass spectrometry data lists: libCSAM lists: RopeBWT2 lists: NetPathMiner lists: BioNumbers lists: leeHom lists: tweeDEseq lists: ProRata lists: Coding Potential Calculator lists: CPTRA lists: MFEprimer lists: Distant Regulatory Elements lists: HGNC lists: GATE lists: SuperPred: Drug classification and target prediction lists: hot scan lists: AltAnalyze - Alternative Splicing Analysis Tool lists: Primer3Plus lists: pairheatmap lists: BioJS lists: ms lims lists: Eukaryotic Linear Motif lists: Proteome Analyst Specialized Subcellular Localization Server lists: HYDEN lists: drFAST lists: GeneFisher lists: GreenPhylDB lists: MiST - Microbial Signal Transduction database lists: Pipeliner lists: Gene Set Enrichment Analysis lists: Piano lists: Weighted Gene Co-expression Network Analysis lists: FastSNP lists: Triplex lists: mrsFAST lists: GenePattern lists: NovelSeq lists: QDNAseq lists: MutDB lists: SplicingCompass lists: deFuse lists: Database of Interacting Proteins (DIP) lists: Assembly Based ReAligner lists: MAGE-TAB lists: ggbio lists: miR-PREFeR lists: NanoStringNorm lists: MIPgen lists: HTqPCR lists: Parseq lists: T-profiler lists: Bpipe lists: jmzTab lists: L-Measure lists: Snakemake lists: PoPoolation lists: MultiPhen lists: PheWAS R Package lists: Quantitative Enrichment of Sequence Tags lists: ALDEx2 lists: INMEX lists: InsertionMapper lists: BSRD lists: SeWeR - SEquence analysis using WEb Resources lists: Segway - a way to segment the genome lists: Stem Cell Discovery Engine lists: TagDust lists: Kdetrees lists: Tree and reticulogram REConstruction lists: NEWT lists: DER Finder lists: BioPig lists: Selectome: a Database of Positive Selection lists: Distributed String Mining Framework lists: PILGRM lists: Apo and Holo structures DataBase lists: MLTreeMap lists: MG-RAST lists: miRNAKey lists: SVseq lists: Small Molecule Pathway Database lists: Information Hyperlinked Over Proteins lists: SVMerge lists: BioSample Database at EBI lists: MetaPhyler lists: SOPRA lists: NCBI BioSystems Database lists: SLIQ lists: G-BLASTN lists: SSPACE lists: AmphoraNet lists: NCBI Structure: Cn3D lists: DELLY lists: RUM lists: STING Report lists: SoyBase lists: SINA lists: Strelka2 lists: RNA-eXpress lists: Percolator: Semi-supervised learning for peptide identification from shotgun proteomics datasets lists: VFS lists: ShoRAH lists: READSCAN lists: ERANGE lists: GeneTalk lists: ORMAN lists: SEECER lists: Scripture lists: SPOT - Biological prioritization after a SNP association study lists: NCBO Annotator lists: CoPub lists: SolexaQA lists: PHAge Search Tool lists: Knime4Bio lists: MethPipe lists: Bis-SNP lists: GobyWeb lists: EMAGE Gene Expression Database lists: FusionMap lists: Yabi lists: GSNAP lists: rQuant lists: MethylViewer lists: DistMap lists: PASS lists: mrFAST lists: Kismeth lists: Stampy lists: TreQ lists: FLASH lists: SAMStat lists: PRINSEQ lists: MethylomeDB lists: SOAPaligner/soap2 lists: TMA Navigator lists: TRANSFAC lists: SeqMap lists: Bambino lists: MicrobesOnline lists: DMRforPairs lists: TIGRFAMS lists: CLIPZ lists: SNPsandGO lists: ToppGene Suite lists: SeqTrace lists: GoSurfer lists: Jellyfish lists: GoFish lists: WEGO - Web Gene Ontology Annotation Plot lists: ngsTools lists: GraphProt lists: SerbGO lists: GoPubMed lists: ccPDB - Compilation and Creation of datasets from PDB lists: DOMMINO - Database Of MacroMolecular INteractiOns lists: SOURCE lists: DistiLD - Diseases and Traits in LD lists: PePr lists: Expression Profiler lists: eQuilibrator lists: DiseaseMeth lists: Dr.VIS - Human Disease-Related Viral Integration Sites lists: FunTree lists: DBETH - Database for Bacterial ExoToxins for Humans lists: BLESS lists: GWASdb lists: HFV Database lists: IndelFR - Indel Flanking Region Database lists: MIPModDB lists: Europe PubMed Central lists: CharProtDB: Characterized Protein Database lists: IDEAL - Intrinsically Disordered proteins with Extensive Annotations and Literature lists: MMMDB - Mouse Multiple tissue Metabolome DataBase lists: ICEberg lists: VirHostNet: Virus-Host Network lists: Cascade lists: Polbase lists: VIRsiRNAdb lists: 959 Nematode Genomes lists: OGEE - Online GEne Essentiality database lists: ProPortal lists: SNPedia lists: Newtomics lists: HotRegion - A Database of Cooperative Hotspots lists: SitEx lists: ScerTF lists: HMM-TM lists: NRG-CING lists: PRED-LIPO lists: InterEvol database lists: SpliceDisease lists: RNA CoSSMos lists: deepSNV lists: PRED-GPCR lists: RecountDB lists: VICUNA lists: ProRepeat lists: MouseBook lists: COEUS lists: Predictive Networks lists: PRED-SIGNAL lists: Flycircuit lists: COLT-Cancer lists: ATRHUNTER lists: GeneTrail lists: epigenomix lists: Pseudomonas Genome Database lists: QCGWAS lists: TSSer lists: UMD-BRCA1/ BRCA2 databases lists: PomBase lists: Phytozome lists: OMPdb lists: GOEAST - Gene Ontology Enrichment Analysis Software Toolkit lists: MSIsensor lists: GWAMA lists: SpliceTrap lists: ViralZone lists: waviCGH lists: MyHits lists: Decombinator lists: CAPS Database lists: ADGO lists: zfishbook lists: EagleView lists: Gene Expression Database lists: SRAdb lists: BEDTools lists: IMGT/GENE-DB lists: RamiGO lists: canSAR lists: IMGT/LIGM-DB lists: PLEXdb - Plant Expression Database lists: COHCAP lists: DARC - Database for Aligned Ribosomal Complexes lists: Immune Epitope Database and Analysis Resource (IEDB) lists: AutismKB lists: RIKEN integrated database of mammals lists: Myrna lists: PhenoM - Phenomics of yeast Mutants lists: BIGpre lists: HIstome: The Histone Infobase lists: TriTrypDB lists: CuticleDB lists: Midbody, Centrosome and Kinetochore lists: SCOP: Structural Classification of Proteins lists: Expression Database in 4D lists: VIDA lists: Database of Arabidopsis Transcription Factors lists: Atlas of Genetics and Cytogenetics in Oncology and Haematology lists: ESEfinder 3.0 lists: agriGO lists: Taipan lists: AgBase lists: Chromosome 7 Annotation Project lists: MEROPS lists: T1DBase lists: Hyper Cell Line Database lists: GenoTan lists: VISTA Browser lists: lobSTR lists: Candidate Genes to Inherited Diseases lists: VISTA Enhancer Browser lists: Gene Array Analyzer lists: Network Analysis, Visualization and Graphing TORonto lists: MuSiC lists: MfunGD - MIPS Mouse Functional Genome Database lists: eTBlast lists: Single Nucleotide Polymorphism Spectral Decomposition (SNPSpD) lists: FGDP lists: hiPathDB - human integrated Pathway DB with facile visualization lists: miRNEST lists: neXtProt lists: NetOGlyc lists: QuasiRecomb lists: GMAP lists: iMir lists: MaCH-Admix lists: SeqBuster lists: LegumeIP lists: DNAtraffic lists: MicroSNiPer lists: Pathema lists: BeeBase lists: Geneious lists: MOSCPHASER lists: SNPinfo Web Server lists: elastix lists: MIRA lists: NEBcutter lists: CopySeq lists: CUPSAT lists: Atlas2 lists: ALLPATHS-LG lists: Velvet lists: HomSI lists: SVDetect lists: omiRas lists: HMCan lists: HapFABIA lists: WEBLOGO lists: ZINBA lists: SICER lists: kmer-SVM lists: MAnorm lists: Pedimap lists: nucleR lists: CEQer lists: MutSig lists: DIANA-LncBase lists: MethMarker lists: PeakRanger lists: PlnTFDB lists: CloudBurst lists: NPS lists: MutationTaster lists: ProDesign lists: OligoArray lists: ArrayAnalysis.org lists: PatMaN lists: SEAL lists: Asterias lists: RACE lists: RobiNA lists: CANGS lists: PlantTFcat lists: LitInspector lists: HSLPred lists: PSAR-Align lists: CancerResource lists: JiffyNet lists: ECHO lists: GPU-Meta-Storms lists: GenoREAD lists: TopHat-Fusion lists: GeneStitch lists: FABIA lists: CPFP lists: MFPaQ lists: ICPL ESIQuant lists: easyRNASeq lists: PREDDIMER lists: NetCoffee lists: SlideSort-BPR lists: miRPlant lists: AlienTrimmer lists: PRIDE Converter 2 lists: SNP ratio test lists: compomics-utilities lists: Allim lists: PLEK lists: ISDTool lists: OBI-Warp lists: LocalAli lists: iceLogo lists: multiplierz lists: AMS lists: NGSmethDB lists: PoolHap lists: DNaseR lists: Btrim lists: COBRApy lists: NAIL lists: CAZy- Carbohydrate Active Enzyme lists: A5-miseq lists: ANNOVAR lists: GENSCAN lists: PhosphoSiteAnalyzer lists: MethylCoder lists: featureCounts lists: LOCAS lists: Scalpel lists: Cell motility lists: Mouse Genome Database lists: CloudAligner lists: HeurAA lists: GSA-SNP lists: seqMINER lists: PolyPhen: Polymorphism Phenotyping lists: rqubic lists: PlantNATsDB - Plant Natural Antisense Transcripts DataBase lists: MitoBreak lists: Cube-DB lists: Death Domain database lists: Telescoper lists: Crossbow lists: MToolBox lists: GENE-counter lists: BEADS lists: PLAN2L lists: INCLUSive lists: CSAR lists: ApiDB CryptoDB lists: MACS lists: NNcon lists: KAVIAR lists: GeneSigDB lists: psRNATarget lists: Composition Profiler lists: MINAS - Metal Ions in Nucleic AcidS lists: EGSEA lists: Crystallography and NMR System (CNS) lists: Morpheus lists: IUPHAR/BPS Guide to Pharmacology lists: RAST Server lists: ProteomicsDB lists: SPEX2 lists: LTR_Finder lists: SCRATCH lists: DSAP lists: PALEOMIX lists: Buccaneer lists: QuantiSNP lists: ProtTest lists: MultiQC lists: GeneWise lists: DISEASES lists: Off-Spotter lists: oligo lists: 3D-footprint lists: SC3 lists: MS-GF+ lists: TISSUES lists: TFBS lists: CHiCAGO lists: Poretools lists: Membrane Protein Explorer lists: FATCAT lists: Bio-tradis lists: ALTER lists: HISAT2 lists: MetaMapR lists: PhyD3 lists: Exonerate lists: primers4clades lists: Fastml lists: Bamtools lists: Genesis lists: DISULFIND lists: EnrichmentMap lists: LoRDEC lists: mentha lists: IDEPI - IDentify EPItopes lists: Oufti lists: FluxModeCalculator lists: eXpression2Kinases lists: SMAGEXP lists: ProCon - PROteomics CONversion lists: Lifebit Deploit lists: TRANSIT lists: Splicing Express lists: Microscopy Image Browser lists: SARTools lists: SPICE lists: DINIES lists: OmicsNet lists: ngsRelate lists: clusterProfiler lists: NetworkAnalyst lists: FRETBursts lists: Thunder STORM lists: ANOCVA lists: ConsensusClusterPlus lists: CIBERSORT lists: CCTOP lists: scran lists: Rsubread lists: Heatmapper lists: BinPacker lists: Subread lists: UMI-tools lists: Goseq lists: PRSice lists: ScaffMatch lists: EMBOSSMatcher lists: JAMM lists: CentroidFold lists: Gigwa lists: FastProject lists: GeSeq lists: ComplexHeatmap lists: PatchDock lists: Proovread lists: trimAl lists: ExPASy ABCD database lists: shinyGEO lists: AmoebaDB lists: Blood Exposome Database lists: STRUCTURE lists: NetPhos lists: Geneshot lists: ProtParam Tool lists: HiC-Pro lists: HingeProt lists: Mousebytes lists: iTOL lists: ChiCMaxima lists: SWISS-MODEL lists: PASTEClassifier lists: R/qtl2 lists: FlowCal lists: Signaling Pathways Project lists: GPS-SUMO lists: Roary lists: SpydrPick lists: ProSA-web lists: SIGNOR lists: MaxAlign lists: REDIportal lists: EpiModel lists: Protein Interactions Calculator lists: rVista lists: Minimap2 lists: PrognoScan lists: Batch Web CD-Search Tool lists: AlgPred lists: GOnet lists: GalaxyWEB lists: GalaxyRefine lists: Annotree lists: khmer lists: E-CRISP lists: Robetta lists: D-GENIES lists: aroma.light lists: Clustal Omega lists: DESeq lists: VICMpred lists: Ray lists: Apollo lists: STAMP lists: discoSnp lists: vcflib lists: IgBLAST lists: BioPerl lists: Genome BioInformatics Research Lab - gff2ps lists: Rainbow lists: Predictions for Entire Proteomes lists: Stacks lists: Clustal W2 lists: RNAhybrid lists: Primer3 lists: SAMtools/BCFtools lists: EBSeq lists: biobambam lists: DIALIGN lists: Unipro UGENE lists: Bowtie 2 lists: Artemis: Genome Browser and Annotation Tool lists: WHAM lists: Database of Secondary Structure Assignments lists: Minia lists: HTSeq lists: RAxML lists: Sickle lists: Segemehl lists: Staden Package lists: Bismark lists: NCBI BLAST lists: Vienna RNA lists: GBrowse lists: ea-utils lists: AmpliconNoise lists: COILS: Prediction of Coiled Coil Regions in Proteins lists: BitSeq lists: HilbertVis lists: VarScan lists: Regulatory Sequence Analysis Tools lists: CD-HIT lists: MACH lists: SOAPsnp lists: ProbCons lists: BEAST lists: Crux tandem mass spectrometry analysis software lists: Pscan-ChIP lists: BRIG lists: tRNAscan-SE lists: CGView lists: Circos lists: FreeBayes lists: Glimmer lists: T-Coffee lists: Oases lists: LIMMA lists: cutadapt lists: SSAKE lists: edgeR lists: OpenMS lists: Flexbar lists: SIFT lists: Mauve lists: Kalign lists: RSEM lists: TopHat lists: DNAcopy lists: phyloseq lists: Trinity lists: AMOS lists: FastTree lists: Cufflinks lists: Prokka lists: PAML lists: CummeRbund lists: GROMACS lists: minet lists: Atac lists: Pilon lists: GMA lists: Nanopolish lists: Krona lists: SeqPrep lists: SortMeRNA lists: THESIAS lists: tximport lists: StoatyDive lists: rCASC lists: precrec lists: IMGT-ONTOLOGY lists: KAT lists: globaltest lists: COPASI lists: CheckM lists: Blobtools lists: NiftyPET lists: SeaView lists: ASHLAR lists: KisSplice lists: metagen lists: BUSCO lists: BLINK lists: bridge lists: Fcirc lists: becas lists: bwtool lists: TGS-GapCloser lists: chimerascan lists: GLUE lists: mosdepth lists: dcmqi lists: SwiftOrtho lists: andi lists: metahdep lists: HaploReg lists: Jalview lists: ScanITD lists: ImaGene lists: BioNix lists: qrqc lists: MeroX lists: sleuth lists: imDEV lists: MiXCR lists: mlgt lists: SMARTdenovo lists: casper lists: miRDB lists: shovill lists: NiftyFit lists: libmgf lists: rbsurv lists: HH-suite lists: affy lists: StatAlign lists: quantsmooth lists: Fiji lists: yaqcaffy lists: Racon lists: h5vc lists: seqbias lists: tensorflow lists: MGnify lists: ngs.plot lists: dyebias lists: Eoulsan lists: Cuffdiff lists: bsseq lists: VEnCode lists: OrthoFinder lists: genomation lists: SymPy lists: eTRIKS lists: ascat lists: Bridger lists: GADMA lists: lumi lists: PIRATE lists: Hippocampome.org lists: HaTSPiL lists: XL-mHG lists: VETA lists: mitopred lists: ropls lists: sabre lists: scanpy lists: icy lists: plgem lists: MethBase lists: biobakery lists: minfi lists: HyPhy lists: MyGene.info lists: EpiEstim lists: NanoSim lists: fracridge lists: TDimpute lists: Pavian lists: SimVascular lists: qcmetrics lists: Laniakea lists: CRISPRcasIdentifier lists: BISE lists: ODAM lists: MRIcron lists: smashpp lists: BSA4Yeast lists: neuroelectro lists: RepeatFiller lists: ShinyLearner lists: docker4seq lists: CRISPR-ERA lists: MAFFT lists: RepeatScout lists: Phenoscape lists: PhenoMeNal lists: multtest lists: TransDecoder lists: les lists: PlotTwist lists: CRISPR-P lists: Telescope lists: charm lists: Warp lists: skewer lists: Human Neocortical Neurosolver lists: ggtree lists: Datanator lists: genehunter-imprinting lists: GraphClust2 lists: eisa lists: scVelo lists: GEMINI lists: beadarray lists: NGSEP lists: ProP Server lists: CandiMeth lists: METAREP lists: scater lists: BioBERT lists: iontree lists: MetaP lists: larvalign lists: UALCAN lists: VAPPER lists: halSynteny lists: EvidenceFinder lists: bcbio-nextgen lists: QuickNII lists: QIIME lists: phantompeakqualtools lists: MCScan lists: pepwheel lists: PathwayMatcher lists: vsn lists: VisR lists: Galaxy scater lists: OpenWorm lists: ffpe lists: timecourse lists: Metascape lists: Bio2BEL lists: RDXplorer lists: ActiveDriver lists: GENCODE lists: CRISPRdirect lists: GeneMarkS-T lists: SPM lists: Bionitio lists: ascend lists: TCW lists: NanoPipe lists: NeuroChaT lists: pheatmap lists: prank lists: Online Peri-Event Time Histogram for Open Ephys lists: kallisto lists: ggplot2 lists: odMLtables lists: glycomedb lists: pickgene lists: GigaSOM.jl lists: pvac lists: EHRtemporalVariability lists: GemSIM lists: lapmix lists: PAFScaff lists: refgenie lists: biospytial lists: EnteroBase lists: QGIS lists: CLIP-Explorer lists: RatMine lists: NMRProcFlow lists: cn.mops lists: SPP lists: seq-annot lists: PsyGeNET lists: PASA lists: UniCarb-DB lists: NormqPCR lists: PhylomeDB lists: SnpHub lists: ReadqPCR lists: circlize lists: HmtVar lists: sim4cc lists: gprege lists: FusionCatcher lists: UniCarbKB lists: clustergrammer lists: clipcrop lists: metabnorm lists: rnaQUAST lists: VirusMINT lists: breseq lists: PerM lists: SnpEff lists: DecGPU lists: e-Driver lists: NCBI BioProject lists: Flye lists: nondetects lists: PEMer lists: VCFtools lists: STAR lists: fastqz lists: SAMTOOLS lists: Neuroscience Information Framework lists: eProbalign lists: dbEST lists: Dali Server lists: Genomic Ranges lists: GenomicFeatures lists: Cistrome lists: SOAPdenovo lists: IRanges lists: BpForms lists: BcForms lists: DIANA-mirPath lists: AthaMap lists: Ancestrymap lists: AutoDock lists: European Genome phenome Archive lists: GEN3VA lists: 4See lists: ABNER lists: Addgene lists: A Classification of Mobile genetic Elements lists: ADMIXTOOLS lists: AETIONOMY lists: ADMIXMAP lists: ALCHEMY lists: Allele Frequencies in Worldwide Populations lists: ABS: A Database of Annotated Regulatory Binding Sites From Orthologous Promoters lists: Alta-Cyclic lists: Alternate splicing gallery lists: Assisted Model Building with Energy Refinement (AMBER) lists: ALOHOMORA lists: AmpliconTagger lists: Molecular Dynamics Workflow (BioKepler) lists: ANDES lists: ALBERT lists: ape lists: ArrayPipe lists: ArrayMiner lists: Aroma.affymetrix lists: ASPEX lists: The Alternatve Splicing Database lists: ASSOCIATIONVIEWER lists: Avogadro lists: AutoAssemblyD lists: BadMedicine lists: BamView lists: BAIT lists: BatMeth lists: AutoDock Vina lists: BARS lists: BCBtoolkit lists: Athena lists: BarraCUDA lists: betaVAEImputation lists: BiG-SLiCE lists: BBSeq lists: SVM based method for predicting beta hairpin structures in proteins lists: BioCarta Pathways lists: BayesEpiModels lists: BiNGO: A Biological Networks Gene Ontology tool lists: BeetleBase lists: BAR lists: BioConda lists: Bioinformatics Toolkit lists: Bionimbus lists: biomaRt lists: Bio++ lists: naiveBayesCall lists: BioSimulations lists: BioPlex lists: Biopieces lists: BRAIN lists: BLAT lists: BS Seeker lists: Breakpointer lists: Canu lists: BioSimulators lists: BRB-ArrayTools lists: bioSyntax lists: CATALYST lists: BOMP: beta-barrel Outer Membrane protein Predictor lists: bioRxiv lists: CAT lists: CCREL lists: BWA lists: CASPAR lists: CARD lists: CATH: Protein Structure Classification lists: CATdb: a Complete Arabidopsis Transcriptome database lists: Cell Image Library (CIL) lists: CEM lists: Cancer Genome Anatomy Project lists: Centrifuge Classifier lists: Bs-Seeker2 lists: ChimeraSlayer lists: ChemSpider lists: BSVF lists: CiLiQuant lists: Chipster lists: CleanEx lists: CHEBI lists: cisTEM lists: CiteFuse lists: clustLasso lists: Chromas lists: ChiRA lists: CNVer lists: CITE-seq-Count lists: CNV-seq lists: circlncRNAnet lists: CMap lists: COGEME Phytopathogenic Fungi and Oomycete EST Database lists: ClinVar lists: ChIPMunk lists: CODEHOP lists: ClustVis lists: CoCo lists: CONTRA lists: Comparative Metatranscriptomics Workflow lists: ComiR lists: CopyDetective lists: ConDeTri lists: Clinotator lists: cortex lists: ClinTrajAn lists: CorMut lists: Coot lists: CRCView lists: CUDASW++ lists: CovalentDock Cloud lists: Chromosome Scale Assembler lists: CYANA lists: Datasets2Tools lists: DBTSS: Database of Transcriptional Start Sites lists: CoryneRegNet lists: CSDeconv lists: CRISPy-web lists: dbSNP lists: ΔG prediction server lists: DGIdb lists: DANPOS2 lists: CorrDrugTumorMSI lists: NCBI database of Genotypes and Phenotypes (dbGap) lists: Dictyostelium discoideum genome database lists: DIAMOND lists: DichroWeb lists: DETONATE lists: DicomTypeTranslator lists: DIME lists: DEXSeq lists: DisProt - Database of Protein Disorder lists: D-EE lists: DAMBE lists: DiffBind lists: DiProGB lists: DOGMA lists: DSK lists: ENIGMA lists: Descriptions of Plant Viruses lists: DOMINE: Database of Protein Interactions lists: Dissect lists: DrivAER lists: Enrichr lists: Variant Effect Predictor lists: EBCall lists: eDMR lists: EMAN lists: Entrez Gene lists: ensembldb lists: Ensembl lists: Epigenomics Workflow on Galaxy and Jupyter lists: Ensembl Genomes lists: epitopepredict lists: DISENTANGLER lists: EpiDISH R package lists: ECLIPSE lists: Experimental Design Assistant lists: EpiGRAPH lists: European Variation Archive (EVA) lists: eQtlBma lists: Eukaryote Genes lists: EXOMEPICKS lists: fineSTRUCTURE lists: Evex lists: Evolutionary Couplings Server lists: Examl lists: NHLBI Exome Sequencing Project (ESP) lists: FlowSOM lists: FireDB lists: FGENESH lists: ExpressYourself lists: fgsea lists: FINDbase Worldwide lists: FateID lists: FluoRender lists: An Integrated Multiple Structure Visualization and Multiple Sequence Alignment Application lists: FlexProt: flexible protein alignment lists: FlyBase lists: FLOSS lists: Full-Length cDNA Database lists: FANTOM DB lists: FragGeneScan lists: FuncAssociate: The Gene Set Functionator lists: FastQC lists: Genome Database for Rosaceae lists: Fugu Genome Project lists: FunRich: Functional Enrichment analysis tool lists: GASSST lists: G-Mo.R-Se lists: GeneCodis lists: GASV lists: FusionHunter lists: Genome Annotation Generator lists: GeneSeeker lists: GenePattern Notebook lists: GeCo3 lists: Gene3D lists: GeMoMa lists: GATK lists: Genome Projector lists: Genomedata lists: Gene Expression Atlas lists: GeneProf lists: Genome Trax lists: GENERECON lists: Genometa lists: GEDIT lists: FunCluster lists: Gibbs Motif Sampler lists: GEMB lists: Genome Reviews lists: GensearchNGS lists: GEPAT lists: Genomic Annotation in Livestock for positional candidate LOci lists: Generic GO Term Finder lists: GermOnline lists: VBASE2 lists: GEO2R lists: GFINDer: Genome Function INtegrated Discoverer lists: Generic GO Term Mapper lists: Google lists: Gene Ontology lists: Genome Aggregation Database lists: Gmove lists: Git lists: GNUMAP lists: G protein receptor interaction feature finding instrument lists: Graph2GO lists: Gaggle lists: GoMapMan lists: Gramene lists: GTDB-Tk lists: GO2MSIG lists: GMcloser lists: Genovar lists: Human Gene Mutation Database lists: H-InvDB lists: Bioinformatic Harvester IV (beta) at Karlsruhe Institute of Technology lists: GRASS lists: HTR lists: International HapMap Project lists: HASTE-project lists: HARSH lists: HAPLOCLUSTERS lists: HSSP lists: Homologous Sequences in Ensembl Animal Genomes lists: Human Splicing Finder lists: HPEPDOCK Server lists: HS-TDT lists: HubMed lists: IBIS: Inferred Biomolecular Interactions Server lists: hyfi: software suite for binding site search lists: HiCUP lists: Human Gene Connectome Server lists: Identifiers.org lists: HUGE - Human Unidentified Gene-Encoded large proteins lists: Hybrid-denovo lists: HINT lists: HUDSEN lists: IntEnz- Integrated relational Enzyme database lists: IMG System lists: HCLUST lists: iDASH lists: HiPipe lists: IMGT/StatClonotype lists: I-TASSER lists: IRESite lists: IMEx - The International Molecular Exchange Consortium lists: IMGT/HLA lists: ImJoy lists: IMGT HighV-QUEST lists: IMGT - the international ImMunoGeneTics information system lists: IsoEM lists: IPD - Immuno Polymorphism Database lists: iPiG lists: IPI lists: Isaac lists: Integr8 : Access to complete genomes and proteomes lists: inGAP lists: ISFinder lists: jmzML lists: Interolog/Regulog Database lists: IsoLasso lists: LAST lists: LOCUSMAP lists: J-Express lists: IsaCGH lists: IMG lists: lncRNAdb lists: InterProScan lists: KGGSeq lists: LDSELECT lists: Magic lists: JGI Genome Portal lists: lme4 lists: MAP lists: OntoQuest lists: Database oDatabase of Predicted Subcellular Localization for Eukaryotic PDB Chainsf Predicted Subcellular Localization for Eukaryotic PDB Chains lists: MACiE lists: LitMiner lists: long-read-tools lists: LOCATE: subcellular localization database lists: LTR_FINDER_parallel lists: Maq lists: MaizeGDB lists: Mammalian Gene Collection lists: Machado lists: LRPath lists: MentaLiST lists: MatrixDB lists: MARRVEL lists: MEBS: Multigenomic Entropy-Based Score lists: Libra lists: LS-SNP/PDB lists: mapDamage lists: Maqview lists: Mascot lists: MAKER lists: MapSplice lists: MetAMOS lists: MethylExtract lists: MBGD - Microbial Genome Database lists: MB-GAN lists: MetaCyc lists: MeQA lists: MEGAHIT lists: Metabolomics Workbench lists: miRBase lists: Metastats lists: MBCluster.Seq lists: metaXplor lists: lsa_slurm lists: MeRIP-PF lists: MendelIHT.jl lists: proMODMatcher lists: mirTools lists: MetaCyto lists: MMAPPR lists: MICSA lists: MIRIAM Resources lists: MaSuRCA lists: UEA sRNA Workbench lists: MetaVelvet lists: miROrtho: the catalogue of animal microRNA genes lists: MERMAID lists: Mspire-Simulator lists: MULTIMAP lists: ML Repo lists: MIP Scaffolder lists: SCIPION lists: MPscan lists: MISA lists: MobiDB lists: MutPred lists: MizBee lists: MRFSEQ lists: MultiLoc lists: MP3 tool lists: Multi-omics Visualization Platform lists: NCBI Probe lists: NeLS lists: MoDIL lists: MPDA lists: Noncoding RNA database lists: Myriads lists: MUMmer lists: Multiple Myeloma survival predictor lists: mrCaNaVaR lists: MULTIDISEQ lists: mzMatch lists: Mouse Phenome Database (MPD) lists: NCBI lists: Ngs backbone lists: NetMHCpan Server lists: miRpathDB lists: NEMBASE lists: Nucleic Acid Database lists: NCBI Genome 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Framework lists: RepeatModeler lists: QuickGO lists: QmRLFS-finder lists: RefSeq lists: The Human Protein Atlas lists: QGene lists: PolyPhred lists: Rampart lists: ResponseNet lists: QUMA lists: QMSIM lists: RAREMETAL lists: Relate lists: ReactomePA lists: RESID lists: RADAR-base lists: Reaper - Demultiplexing trimming and filtering sequencing data lists: R-SAP lists: Research-tested Intervention Programs (RTIPs) lists: RNA FRABASE - RNA FRAgments search engine and dataBASE lists: Reptile lists: Rdisop lists: RNA-SeQC lists: RNA Virus Database lists: RESCUE-ESE lists: REDItools lists: RegulonDB lists: SeqExpress lists: Scansite lists: RiboTaper lists: SALT lists: riborex lists: REDfly Regulatory Element Database for Drosophilia lists: rna-stability lists: RNAplex lists: rSNP Guide lists: SVA lists: RightField lists: runBioSimulations lists: SAMMate lists: SeqtrimNEXT lists: rSeq lists: SeqEM lists: ROMPREV lists: SeqSaw lists: SHARCGS lists: SAFA Footprinting Software lists: SHELX lists: sapFinder lists: QuPath lists: SIBLINK lists: Seqtk lists: SEEK lists: SMRT View lists: SKAT lists: SimRare lists: SeQuiLa lists: SGA lists: SASQUANT lists: Sherman lists: SilkDB lists: FASTSLINK lists: SASGENE lists: SILVA lists: SGD lists: ShinyGO lists: SimSeq lists: SIDER lists: SMI Services lists: Sniffles lists: STEPS lists: SNP HITLINK lists: SOAPnuke lists: SGN lists: SIBMED lists: SIMULATE lists: rnaSPAdes lists: SpliceMap lists: SMART lists: SnoopCGH lists: SynTView lists: SIMPED lists: Supersplat lists: SnpSift lists: SISSRs lists: Sybil lists: Solas lists: SNPTEST lists: SISYPHUS lists: ASC lists: SOAPfusion lists: TAndem Splice Site DataBase lists: SoupX lists: StSNP lists: T-lex lists: SWEEP lists: SynergyFinder lists: topGO lists: TAPIR: target prediction for plant microRNAs lists: TDT-PC lists: TDR Targets Database lists: SpoTyping lists: ShortFuse lists: SWISS-2DPAGE lists: Spot lists: TAGS lists: SYFPEITHI: A Database for MHC Ligands and Peptide Motifs lists: SUMSTAT lists: TMAJ lists: TASSEL lists: TreeDyn lists: TropGENE DB lists: TB PORTALS lists: SwissTree lists: tradeSeq lists: FLUX CAPACITOR lists: UNAFold lists: Transporter Classification Database lists: ApiDB ToxoDB lists: Trowel lists: TopFIND lists: TRAL lists: Trim Galore lists: Biological General Repository for Interaction Datasets (BioGRID) lists: IQ-TREE lists: VirusSeq lists: Tool recommender system in Galaxy lists: V-Phaser 2 lists: SPIKE lists: Trans-ABySS lists: TRiCoLOR lists: TomoMiner lists: variancePartition lists: TRACESPipe lists: UTRdb/UTRsite lists: UniParc lists: TWOLOC lists: USeq lists: Zebrafish Information Network (ZFIN) lists: XPN lists: TransmiR lists: Webproanalyst lists: UTGB Toolkit lists: VAAST lists: VirusHunter lists: Yeast Search for Transcriptional Regulators And Consensus Tracking lists: zUMIs lists: VaDiR lists: WSsas - Web Service for the SAS tool lists: VFDB - Virulence Factors of Bacterial Pathogens lists: Gene Index Project lists: Vector Alignment Search Tool lists: Vmatch lists: WEIGHTED FDR lists: Xenbase lists: xia2 pipeline lists: YASARA lists: Visualization and Analysis of Networks containing Experimental Data (VANTED) lists: VisSR lists: dbEST lists: DESeq2 lists: DNA DataBank of Japan (DDBJ) lists: FASTX-Toolkit lists: Trimmomatic lists: VIPERdb lists: PhenStat lists: ABySS lists: Integrative Genomics Viewer lists: Human Disease Ontology lists: LINKAGE lists: ConSurf Database lists: Protein Information Resource lists: PredictNLS lists: tRNAscan-SE lists: VeryFastTree lists: RSEM lists: Emboss Water lists: MEtabolomes, TRaits, and INteractions-Knowledge Graph lists: Drybench lists: ProtBed lists: SwapSeq is listed by: Debian is listed by: ELIXIR Tools and Data Services Registry is affiliated with: ELIXIR Tools and Data Services Registry is related to: ms-utils.org is related to: SUP |
Danish Ministry of Higher Education and Science ; European Union Horizon 2020 ELIXIR-EXCELERATE grant 676559 |
DOI:10.1186/s13059-019-1772-6 PMID:26538599 |
Free, Freely available | biotools:bio.tools, r3d100013668 | https://github.com/bio-tools/biotoolsRegistry/, https://bio.tools/bio.tools, https://doi.org/10.17616/R31NJN1G | http://bio.tools | SCR_014695 | SciCrunch Registry | 2026-11-07 11:57:54 | 29 | |||||
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PAZAR Resource Report Resource Website 10+ mentions |
PAZAR (RRID:SCR_005410) | PAZAR | data or information resource, data repository, database, service resource, software resource, storage service resource | Database that unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. The flexible PAZAR schema permits the representation of diverse information derived from experiments ranging from biochemical protein-DNA binding to cellular reporter gene assays. Data collections can be made available to the public, or restricted to specific system users. The data ''boutiques'' within the shopping-mall-inspired system facilitate the analysis of genomics data and the creation of predictive models of gene regulation., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | transcription factor, target gene, regulatory sequence, transcription factor profile, annotation, sequence, profile, transcription factor binding profile, chip, chip-seq, gene, cis-regulatory element, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of British Columbia; British Columbia; Canada has parent organization: SourceForge |
PMID:18971253 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00540, biotools:pazar | https://bio.tools/pazar | SCR_005410 | SciCrunch Registry | 2026-11-07 11:55:55 | 32 |
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