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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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AIDA Toolkit Resource Report Resource Website 1+ mentions |
AIDA Toolkit (RRID:SCR_005914) | software toolkit, web service, software resource, data access protocol | A generic set of components that can perform a variety of tasks, such as learn new pattern recognition models, perform specialized search on resource collections, and store knowledge in a repository. W3C standards are used to make data accessible and manageable with semantic web technologies such as OWL, RDF(S), and SKOS. The AIDA Toolkit is directed at groups of knowledge workers that cooperatively search, annotate, interpret, and enrich large collections of heterogeneous documents from diverse locations. The server offers services for: text indexing and statistics, metadata storage and querying, thesaurus reasoning, annotation, text retrieval, spelling correction, synonym detection, and model learning. | software toolkit, web service, search, learning, storage, workflow, text indexing, text statistics, metadata storage, metadata querying, thesaurus reasoning, annotation, text retrieval, spelling correction, synonym detection, model learning | is related to: Taverna | Open source, Available as a web service, Available for download | nlx_149497 | http://adaptivedisclosure.org/aida/ | SCR_005914 | Adaptive Information Disclosure Application Toolkit | 2026-08-11 09:41:20 | 1 | |||||||
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Roth Laboratory Resource Report Resource Website 1+ mentions |
Roth Laboratory (RRID:SCR_005711) | Roth Lab | portal, data or information resource, organization portal, software resource, laboratory portal | The Roth Laboratory is designing and interpreting large-scale experiments to understand pathway structure and its relationship to phenotype and human disease. Software for research focused on a specific research goal is available. Current experimental interests: * Exploiting parallel sequencing technology to phenotype all pairwise gene deletion combinations in S. cerevisiae, with initial application to genes involved in transcription. * Generation of S. cerevisiae strains carrying dozens of chosen targeted deletions, with initial application to delete all ABC transporters imparting multidrug resistance. * Targeted insertion of gene sets encoding entire human pathways into S. cerevisiae, with initial application to genes involved in drug metabolism. Current computational interests: * Systematic analysis of genetic interaction to reveal redundant systems and order of action in genetic pathways * Integrating large-scale studies - including phenotype, genetic epistasis, protein-protein and transcription-regulatory interactions and sequence patterns - to quantitatively assign function to genes and guide experimentation and disease association studies. * Alternative splicing and its relationship to protein interaction networks. | gene, pathway, phenotype, disease, transcription, drug metabolism, drug, metabolism, protein-protein interaction, transcription-regulatory interaction, protein interaction, protein |
has parent organization: University of Toronto; Ontario; Canada has parent organization: Harvard Medical School; Massachusetts; USA is parent organization of: FuncAssociate: The Gene Set Functionator |
nlx_149163 | http://llama.med.harvard.edu | SCR_005711 | 2026-08-11 09:41:11 | 5 | ||||||||
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InterProScan Resource Report Resource Website 5000+ mentions |
InterProScan (RRID:SCR_005829) | service resource, data analysis software, software application, analysis service resource, web service, software resource, data analysis service, production service resource, data processing software, data access protocol | Software package for functional analysis of sequences by classifying them into families and predicting presence of domains and sites. Scans sequences against InterPro's signatures. Characterizes nucleotide or protein function by matching it with models from several different databases. Used in large scale analysis of whole proteomes, genomes and metagenomes. Available as Web based version and standalone Perl version and SOAP Web Service. | functional, analysis, sequence, protein, nucleotide, predict, presence, domain, site, proteome, genome, metagenome, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Gene Ontology is related to: RARTF is related to: InterPro is related to: LegumeIP is related to: UniProtKB has parent organization: European Bioinformatics Institute |
European Union ; Biotechnology and Biological Sciences Research Council ; EMBL |
PMID:15980438 PMID:17202162 PMID:24451626 |
Free, Available for download, Freely available | OMICS_01479, biotools:interproscan_4, nlx_149337 | https://www.ebi.ac.uk/interpro/download.html, https://bio.tools/interproscan_4 | SCR_005829 | InterProScan Sequence Search, InterProScan 2, InterProScan 3, InterProScan 4, InterProScan 5 | 2026-08-11 09:41:12 | 7512 | |||||
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GeneMANIA Resource Report Resource Website 1000+ mentions |
GeneMANIA (RRID:SCR_005709) | GeneMANIA | service resource, analysis service resource, data or information resource, database, software resource, data analysis service, production service resource | Data analysis service to predict the function of your favorite genes and gene sets. Indexing 1,421 association networks containing 266,984,699 interactions mapped to 155,238 genes from 7 organisms. GeneMANIA interaction networks are available for download in plain text format. GeneMANIA finds other genes that are related to a set of input genes, using a very large set of functional association data. Association data include protein and genetic interactions, pathways, co-expression, co-localization and protein domain similarity. You can use GeneMANIA to find new members of a pathway or complex, find additional genes you may have missed in your screen or find new genes with a specific function, such as protein kinases. Your question is defined by the set of genes you input. If members of your gene list make up a protein complex, GeneMANIA will return more potential members of the protein complex. If you enter a gene list, GeneMANIA will return connections between your genes, within the selected datasets. GeneMANIA suggests annotations for genes based on Gene Ontology term enrichment of highly interacting genes with the gene of interest. GeneMANIA is also a gene recommendation system. GeneMANIA is also accessible via a Cytoscape plugin, designed for power users. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene, association data, protein interaction, genetic interaction, pathway, co-expression, co-localization, protein, software library, statistical analysis, term enrichment, analysis, browser, gene ontology, gene predicting, gene prioritization, database or data warehouse, other analysis, interaction browser, protein-protein interaction, interaction, FASEB list |
is listed by: Gene Ontology Tools is related to: Cytoscape is related to: Gene Ontology is related to: PSICQUIC Registry has parent organization: University of Toronto; Ontario; Canada |
Genome Canada ; Ontario Ministry of Research and Innovation 2007-OGI-TD-05 |
PMID:20576703 PMID:18613948 PMID:20926419 |
Open unspecified license, Free for academic use | nlx_149159, r3d100013978 | https://doi.org/10.17616/R31NJNA2 | SCR_005709 | 2026-08-11 09:41:10 | 4535 | |||||
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Automated Image Registration Resource Report Resource Website 10+ mentions |
Automated Image Registration (RRID:SCR_005944) | AIR | software application, alignment software, software toolkit, image analysis software, registration software, software resource, software library, data processing software | A tool for automated registration of 3D (and 2D) images within and across subjects and within and sometimes across imaging modalities. The AIR library can easily incorporate automated image registration into site specific programs adapted to your particular needs. | registration, alignment |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps |
GNU General Public License | nif-0000-00260 | http://www.nitrc.org/projects/air | SCR_005944 | 2026-08-11 09:41:20 | 29 | |||||||
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Whatizit Resource Report Resource Website 1+ mentions |
Whatizit (RRID:SCR_005824) | Whatizit | service resource, analysis service resource, web service, software resource, data analysis service, production service resource, data access protocol | A text processing system that allows you to do textmining tasks on text. It is great at identifying molecular biology terms and linking them to publicly available databases. Whatizit is also a Medline abstracts retrieval/search engine. Instead of providing the text by Copy&Paste, you can launch a Medline search. The abstracts that match your search criteria are retrieved and processed by a pipeline of your choice. Whatizit is also available as 1) a webservice and as 2) a streamed servlet. The webservice allows you to enrich content within your website in a similar way as in the wikipedia. The streamed servlet allows you to process large amounts of text. | textual analysis, protein, gene, gene ontology, text-mining, annotation, literature analysis |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: UniProt is related to: MEDLINE is related to: NCBI Taxonomy has parent organization: European Bioinformatics Institute |
Free for academic use | OMICS_01200, nlx_149329 | http://www.ebi.ac.uk/webservices/whatizit | SCR_005824 | 2026-08-11 09:41:12 | 8 | |||||||
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UM-BBD Resource Report Resource Website 1+ mentions |
UM-BBD (RRID:SCR_005787) | UM-BBD, UM-BBD enzymeID, UM-BBD pathwayID, UM-BBD reactionID, UM-BBD ruleID | service resource, analysis service resource, data or information resource, database, data analysis service, production service resource, data set | THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 27, 2014. Database containing information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. Its goal is to provide information on microbial enzyme-catalyzed reactions that are important for biotechnology. The reactions covered are studied for basic understanding of nature, biocatalysis leading to specialty chemical manufacture, and biodegradation of environmental pollutants. Individual reactions and metabolic pathways are presented with information on the starting and intermediate chemical compounds, the organisms that transform the compounds, the enzymes, and the genes. The present database has been successfully used to teach enzymology and use of biochemical Internet information resources to advanced undergraduate and graduate students, and is being expanded primarily with the help of such students. In addition to reactions and pathways, this database also contains Biochemical Periodic Tables and a Pathway Prediction System. * Search the UM-BBD for compound, enzyme, microorganism, pathway, or BT rule name; chemical formula; chemical structure; CAS Registry Number; or EC code. * Go to Pathways and Metapathways in the UM-BBD * Lists of 203 pathways; 1400 reactions; 1296 compounds; 916 enzymes; 510 microorganism entries; 245 biotransformation rules; 50 organic functional groups; 76 reactions of naphthalene 1,2-dioxygenase; 109 reactions of toluene dioxygenase; Graphical UM-BBD Overview; and Other Graphics (Metapathway and Pathway Maps and Reaction Mechanisms). | enzyme, biocatalysis, biodegredation, chemical, pathway, reaction, microorganism, image, chemical compound, gene, enzymology | has parent organization: University of Minnesota Twin Cities; Minnesota; USA | Minnesota Supercomputing Institute ; Lhasa Limited ; University of Minnesota; Minnesota; USA ; European Union FP6 ALARM project ; NIH ; NSF 0543416; DOE DE-FG02-01ER63268; NIGMS R01GM56529; NSF 9630427 |
PMID:19767608 PMID:16381924 PMID:12519997 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-03607, r3d100011317 | https://doi.org/10.17616/R33D0V | SCR_005787 | UM-BBD pathwayID, University of Minnesota Biocatalysis and Biodegradation Database, UM-BBD reactionID, Biocatalysis/Biodegradation Database, University of Minnesota Biocatalysis/Biodegradation Database, UM-BBD ruleID, Univeristy of Minnesota Biocatalysis/Biodegradation Database, UM-BBD enzymeID | 2026-08-11 09:41:12 | 9 | ||||
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DiseaseMeth Resource Report Resource Website 10+ mentions |
DiseaseMeth (RRID:SCR_005942) | service resource, data or information resource, storage service resource, database, data repository | Human disease methylation database. DiseaseMeth version 2.0 is focused on aberrant methylomes of human diseases. Used for understanding of DNA methylation driven human diseases. | disease, methylation, dna methylation, genome, gene, epigenetics, epigenomics, methylome, bio.tools |
is listed by: 3DVC is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Harbin Medical University; Heilongjiang; China |
National Natural Science Foundation of China ; Natural Science Foundation of Heilongjiang Province ; State Key Laboratory of Urban Water Resource and Environment ; Scientific Research Fund of Heilongjiang Provincial Education Department |
PMID:22135302 PMID:27899673 |
Free,Freely available | OMICS_01838, nlx_151289, biotools:diseasemeth, SCR_017488 | http://bioinfo.hrbmu.edu.cn/diseasemeth, https://bio.tools/diseasemeth | http://202.97.205.78/diseasemeth/ | SCR_005942 | , Disease Meth-The Human Disease Methylation Database, DiseaseMeth database, DiseaseMeth version 2.0 | 2026-08-11 09:41:14 | 44 | ||||
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DistiLD - Diseases and Traits in LD Resource Report Resource Website 1+ mentions |
DistiLD - Diseases and Traits in LD (RRID:SCR_005943) | DistiLD | service resource, analysis service resource, data or information resource, database, data analysis service, production service resource | The DistiLD database aims to increase the usage of existing genome-wide association studies (GWAS) results by making it easy to query and visualize disease-associated SNPs and genes in their chromosomal context. The database performs three important tasks: # published GWAS are collected from several sources and linked to standardized, international disease codes ICD10 codes) # data from the International HapMap Project are analyzed to define linkage disequilibrium (LD) blocks onto which SNPs and genes are mapped # the web interface makes it easy to query and visualize disease-associated SNPs and genes within LD blocks. Users can query the database by diseases, SNPs or genes. No matter which of the three query modes was used, an intermediate page will be shown listing all the studies that matched the search with a link to the corresponding publication. The user can select either all studies related to a certain disease or one specific study for which to view the related LD blocks. The DistiLD resource integrates information on: * Associations between Single Nucleotide Polymorphisms (SNPs) and diseases from genome-wide association studies (GWAS) * Links between SNPs and genes based on linkage disequilibrium (LD) data from HapMap For convenience, we provide the complete datasets as two (zipped) tab-delimited files. The first file contains GWAS results mapped to LD blocks. The second file contains all SNPs and genes assigned to each LD block. | disease, mutation, gene, linkage disequilibrium, trait, genome-wide association study, single nucleotide polymorphism, chromosomal region, chromosome, linkage disequilibrium block, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: International HapMap Project has parent organization: University of Copenhagen; Copenhagen; Denmark |
Novo Nordisk Foundation Center for Protein Research | PMID:22058129 | Files are published under the Creative Commons Attribution v3 License | biotools:distild, nlx_151291 | https://bio.tools/distild | SCR_005943 | DistiLD - Diseases & Traits in LD, Diseases and Traits In Linkage Disequilibrium blocks, Diseases and Traits In Linkage Disequilibrium, DistiLD Database, DistiLD - Diseases Traits in LD | 2026-08-11 09:41:13 | 5 | ||||
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UCSC Genome Browser Resource Report Resource Website 10000+ mentions Rating or validation data |
UCSC Genome Browser (RRID:SCR_005780) | portal, project portal, service resource, data or information resource, database | Portal to interactively visualize genomic data. Provides reference sequences and working draft assemblies for collection of genomes and access to ENCODE and Neanderthal projects. Includes collection of vertebrate and model organism assemblies and annotations, along with suite of tools for viewing, analyzing and downloading data. | Reference, sequence, assembly, collection, genome, visualize, genomic, data, ENCODE, Neanderthal, project, sequencing |
is used by: VizHub is used by: Blueprint Epigenome is used by: QmRLFS-finder is used by: International Human Epigenome Consortium Data Portal is used by: iPiG is listed by: re3data.org is listed by: OMICtools is listed by: Educational Resources in Neuroscience is listed by: SoftCite is related to: HEXEvent is related to: PicTar is related to: Phenotree is related to: Enhancer Trap Line Browser is related to: CistromeFinder is related to: ENCODE is related to: Human Epigenome Atlas is related to: ENCODE is related to: BigWig and BigBed is related to: PhenCode is related to: doRiNA is related to: ISCA Consortium is related to: WashU Epigenome Browser is related to: CRISPOR is related to: liftOver is related to: kent has parent organization: University of California at Santa Cruz; California; USA works with: TarBase works with: bedGraphToBigWig |
UC BIOTEuropean UnionH ; Alfred P. Sloan Foundation ; David and Lucille Packard Foundation ; NIH ; HHMI ; CISI ; NHGRI ; DOE ; NSF DBI 9809007; NIGMS GM52848 |
PMID:12045153 PMID:22908213 PMID:23155063 |
OMICS_00926, SCR_017502, nif-0000-03603, SciEx_217, SCR_012479, r3d100010243 | http://genome.cse.ucsc.edu, https://doi.org/10.17616/R3RK5C | SCR_005780 | The Human Genome Browser at UCSC, UCSC Genome Browser Group, University of California at Santa Cruz Genome Browser, UCSC Genome Bioinformatics | 2026-08-11 09:41:12 | 11041 | ||||||
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VBRC Resource Report Resource Website 10+ mentions |
VBRC (RRID:SCR_005971) | VBRC | service resource, analysis service resource, data or information resource, storage service resource, database, data analysis service, production service resource, data repository | One of eight Bioinformatics Resource Centers nationwide providing comprehensive web-based genomics resources including a relational database and web application supporting data storage, annotation, analysis, and information exchange to support scientific research directed at viruses belonging to the Arenaviridae, Bunyaviridae, Filoviridae, Flaviviridae, Paramyxoviridae, Poxviridae, and Togaviridae families. These centers serve the scientific community and conduct basic and applied research on microorganisms selected from the NIH/NIAID Category A, B, and C priority pathogens that are regarded as possible bioterrorist threats or as emerging or re-emerging infectious diseases. The VBRC provides a variety of analytical and visualization tools to aid in the understanding of the available data, including tools for genome annotation, comparative analysis, whole genome alignments, and phylogenetic analysis. Each data release contains the complete genomic sequences for all viral pathogens and related strains that are available for species in the above-named families. In addition to sequence data, the VBRC provides a curation for each virus species, resulting in a searchable, comprehensive mini-review of gene function relating genotype to biological phenotype, with special emphasis on pathogenesis. | virus, arenaviridae, bunyaviridae, filoviridae, flaviviridae, paramyxoviridae, poxviridae, togaviridae, blast, ortholog, variation, sequence analysis, genome, gene, epidemiology, bioinformatics resource center, phenotype, pathogenesis, pathogen, annotation, genomics |
has parent organization: University of Alabama at Birmingham; Alabama; USA has parent organization: University of Victoria; British Columbia; Canada is parent organization of: Hepatitis C Virus Database (HCVdb) |
NIAID contract HHSN266200400036C | r3d100012088, nif-0000-03632 | https://doi.org/10.17616/R31M1P | SCR_005971 | Viral Bioinformatics Resource Center | 2026-08-11 09:41:14 | 18 | ||||||
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BIIT - Bioinformatics Algorithmics and Data Mining Group Resource Report Resource Website 10+ mentions |
BIIT - Bioinformatics Algorithmics and Data Mining Group (RRID:SCR_005690) | BIIT Research group | portal, software application, data or information resource, text-mining software, organization portal, software resource, department portal | The Bioinformatics, Algorithmics, and Data Mining group BIIT lead by prof. Jaak Vilo is a joint research group between the Department of Computer Science (University of Tartu), Quretec, and the Estonian Biocenter. Our main research topics and capabilities include the gene regulation, gene expression data analysis, biological data mining, systems biology, combinatorial pattern matching, developing software for biomedical research databases, as well as partnering in stem cell and cancer related projects. Software * MEM - Multi-Experiment-Matrix -- large-scale gene expression data queries and mining (Genome Biology 2009) * g:Profiler family of tools for functional assessment of gene groups, gene ID mappings, orthology and expression similarity searches. (NAR web server issue 2007) * KEGGanim - visualisation of high-throughput data on biological pathway charts (Bioinformatics, 2007) * GraphWeb - a tool for mining large biological networks (NAR Web server issue 2008) * FunGenES data atlas * More software tools | gene regulation, gene expression, data analysis, biological, data mining, systems biology, combinatorial pattern matching, software, biomedical research, stem cell, cancer |
has parent organization: University of Tartu; Tartu; Estonia is parent organization of: GraphWeb is parent organization of: g:Profiler |
nlx_149141 | http://biit.cs.ut.ee/about/main | SCR_005690 | BIIT - Bioinformatics Algorithmics Data Mining Group, BIIT Group - Institute of Computer Science | 2026-08-11 09:41:10 | 10 | |||||||
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CIPF Bioinformatics and Genomics Department Resource Report Resource Website 1+ mentions |
CIPF Bioinformatics and Genomics Department (RRID:SCR_005692) | CIPF Bioinformatics and Genomics | institution, portal, data or information resource, organization portal, department portal | Biomedicine can only be understood in the context of genomics and with the concourse of bioinformatics. Our department aims to tackle biomedical problems from a system's biology perspective. Following this, the general objective we seek through the main lines of research is to relate the mutations (Pharmacogenomics and Comparative Genomics) to their effect at cellular and phenotypic level (Functional Genomics) trying to understand the mechanism of action (Structural Genomics). Systems Biology Genes operate within an intricate network of interactions that we have only recently started to envisage. Many higher-order levels of interaction are continuously being discovered. In this scenario we are interested in developing methods and tools which can help to understand large-scale experiments from a systems biology perspective. Comparative genomics We are interested in the analysis of patterns and processes occurred during the evolution of our genome, and in the application of the evolutionary thought in human health and disease. * Adaptive Human Evolution * Evolutionary Pharmacogenetics * SNP's and Human Disease Structural genomics Our Unit aims to develop and apply computational methods for understanding the molecular mechanisms of cell regulation beyond proteins. In particular, we apply our methods to study the interaction of small chemical compounds with proteins and to characterize their molecular actions. We are also developing methods for RNA 3D structure prediction with the aim of applying them to understand the effects of non-coding RNA molecules. Finally, in collaboration with experimentalists, we are working in determining the first ever 3D structure of a genomic domain in human. | genomics, bioinformatics |
has parent organization: Principe Felipe Research Centre; Valencia; Spain is parent organization of: Babelomics |
nlx_149143 | SCR_005692 | CIPF Department of Bioinformatics, CIPF Bioinformatics Genomics | 2026-08-11 09:41:18 | 5 | ||||||||
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SeqGSEA Resource Report Resource Website 10+ mentions |
SeqGSEA (RRID:SCR_005724) | SeqGSEA | data analysis software, data processing software, software resource, software application | Software package that provides methods for gene set enrichment analysis of high-throughput RNA-Seq data by integrating differential expression and splicing. It uses negative binomial distribution to model read count data, which accounts for sequencing biases and biological variation. Based on permutation tests, statistical significance can also be achieved regarding each gene''s differential expression and splicing, respectively. | differential expression, gene expression, gene set enrichment, rna-seq, sequencing, splicing |
is listed by: OMICtools has parent organization: Bioconductor |
GNU General Public License, v3 or newer | OMICS_02251 | SCR_005724 | SeqGSEA - Gene Set Enrichment Analysis (GSEA) of RNA-Seq Data: integrating differential expression and splicing | 2026-08-11 09:41:11 | 36 | |||||||
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Onto-Translate Resource Report Resource Website 1+ mentions |
Onto-Translate (RRID:SCR_005725) | Onto-Translate | service resource, analysis service resource, data or information resource, database, data analysis service, production service resource | In the annotation world, the same piece of information can be stored and viewed differently across different databases. For instance, more than one Affymetrix probe ID can refer to the same GenBank sequence (accession number) and more than one nucleotide sequence from GenBank can be grouped in a single UniGene cluster. The result of Onto-Express depends on whether the input list contains Affymetrix probe IDs, GenBank accession numbers or UniGene cluster IDs. The user has to be aware of relations between the different forms of the data in order to interpret correctly the results. Even if the user is aware of the relationships and knows how to convert them, most existing tools allow conversions of individual genes. Onto-Translate is a tool that allows the user to perform easily such translations. Affymetrix probe IDs, etc., translate GO terms into other identifiers like GenBank accession number, Uniprot IDs. User account required. Platform: Online tool | annotation, gene, analysis, database or data warehouse, other analysis, affymetrix probe id, affymetrix, probe id, translate go terms into other identifiers like genbank accession number, genbank accession number, uniprot id, gene ontology, translate |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Wayne State University; Michigan; USA |
PMID:15215428 | Free for academic use | nlx_149182 | SCR_005725 | 2026-08-11 09:41:11 | 3 | |||||||
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ToppGene Suite Resource Report Resource Website 1000+ mentions |
ToppGene Suite (RRID:SCR_005726) | service resource, portal, analysis service resource, data or information resource, database, resource, data analysis service, production service resource | ToppGene Suite is a one-stop portal for gene list enrichment analysis and candidate gene prioritization based on functional annotations and protein interactions network. ToppGene Suite is a one-stop portal for (i) gene list functional enrichment, (ii) candidate gene prioritization using either functional annotations or network analysis and (iii) identification and prioritization of novel disease candidate genes in the interactome. Functional annotation-based disease candidate gene prioritization uses a fuzzy-based similarity measure to compute the similarity between any two genes based on semantic annotations. The similarity scores from individual features are combined into an overall score using statistical meta-analysis. | gene portal, enrichment analysis, functional annotation, gene prioritization, protein interaction, bio.tools, FASEB list |
is listed by: Gene Ontology Tools is listed by: NIDDK Information Network (dkNET) is listed by: GUDMAP Ontology is listed by: Debian is listed by: bio.tools is related to: Gene Ontology is related to: ToppCluster |
State of Ohio Computational Medicine Center ODD TECH 04-042; NIDDK 1U01DK70219; NIDDK P30DK078392 |
PMID:19465376 | Free for academic use | nlx_149183, biotools:toppgene_suite | https://bio.tools/toppgene_suite | SCR_005726 | ToppGene | 2026-08-11 09:41:18 | 1131 | |||||
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TAIR Keyword Browser Resource Report Resource Website 10+ mentions |
TAIR Keyword Browser (RRID:SCR_005687) | TAIR Keyword Browser | service resource, analysis service resource, data or information resource, database, data analysis service, production service resource | TAIR Keyword Browser searches and browses for Gene Ontology, TAIR Anatomy, and TAIR Developmental stage terms, and allows you to view term details and relationships among terms. It includes links to genes, publications, microarray experiments and annotations associated with the term or any children terms. Platform: Online tool | gene ontology, gene, publication, microarray, annotation, cellular component, biological process, molecular function, plant, growth, development, stage, anatomical entity, anatomy, ontology, browser, ontology or annotation browser |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: TAIR |
Free for academic use | nlx_149132 | http://www.arabidopsis.org/servlets/Search?action=new_search&type=keyword | SCR_005687 | TAIR Keyword Search and Browse, The Arabidopsis Information Resource Keyword Browser | 2026-08-11 09:41:18 | 37 | ||||||
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Brain Networks Resource Report Resource Website 1+ mentions |
Brain Networks (RRID:SCR_005841) | Brain Networks | data analysis software, software application, source code, software resource, data processing software | Brain Networks: Code to perform network analysis on brain imaging data. | brain, imaging, network analysis, brain imaging, neuroimaging | has parent organization: SourceForge | PMID:21031030 | Open unspecified license - GNU General Public License (GPL) | nlx_149364 | SCR_005841 | brainnetworks | 2026-08-11 09:41:12 | 1 | ||||||
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BLESS Resource Report Resource Website 10+ mentions |
BLESS (RRID:SCR_005963) | BLESS | data analysis software, software application, algorithm resource, software resource, data processing software, sequence analysis software | Software tool for Bloom-filter-based error correction for next-generation sequencing (NGS) reads. The algorithm produces accurate correction results with much less memory. | c++, next-generation sequencing, bloom-filter, error correction, ngs, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:24451628 | GNU General Public License v3 | OMICS_02246, biotools:bless | https://bio.tools/bless | SCR_005963 | BLoom-filter-based Error correction Solution for high-throughput Sequencing reads, BLESS - Bloom-filter-based Error Correction Tool for NGS reads | 2026-08-11 09:41:14 | 46 | |||||
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Pandora - Protein ANnotation Diagram ORiented Analysis Resource Report Resource Website 1+ mentions |
Pandora - Protein ANnotation Diagram ORiented Analysis (RRID:SCR_005686) | Pandora | service resource, analysis service resource, data or information resource, database, data analysis service, production service resource | With PANDORA, you can search for any non-uniform sets of proteins and detect subsets of proteins that share unique biological properties and the intersections of such sets. PANDORA supports GO annotations as well as additional keywords (from UniProt Knowledgebase, InterPro, ENZYME, SCOP etc). It is also integrated into the ProtoNet system, thus allowing testing of thousands of automatically generated protein families. Note that PANDORA replaces the ProtoGO browser developed by the same group. Platform: Online tool | protein, annotation, mass spectrometry, ontology or annotation browser |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: Hebrew University of Jerusalem; Jerusalem; Israel |
Israeli Ministry of Defense ; Hebrew University of Jerusalem; Jerusalem; Israel |
PMID:14500825 | Free for academic use | nlx_149131 | SCR_005686 | Protein ANnotation Diagram ORiented Analysis | 2026-08-11 09:41:10 | 2 |
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