Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Candidate Genes to Inherited Diseases Resource Report Resource Website 1+ mentions |
Candidate Genes to Inherited Diseases (RRID:SCR_008190) | G2D | production service resource, data analysis service, service resource, database, analysis service resource, data or information resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A database of candidate genes for mapped inherited human diseases. Candidate priorities are automatically established by a data mining algorithm that extracts putative genes in the chromosomal region where the disease is mapped, and evaluates their possible relation to the disease based on the phenotype of the disorder. Data analysis uses a scoring system developed for the possible functional relations of human genes to genetically inherited diseases that have been mapped onto chromosomal regions without assignment of a particular gene. Methodology can be divided in two parts: the association of genes to phenotypic features, and the identification of candidate genes on a chromosonal region by homology. This is an analysis of relations between phenotypic features and chemical objects, and from chemical objects to protein function terms, based on the whole MEDLINE and RefSeq databases. | function, gene, genetic, chromosome, disease, disorder, genome, homology, human, phenotype, protein, region, candidate gene, database, data warehouse, data set, bio.tools |
is listed by: 3DVC is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: European Molecular Biology Laboratory has parent organization: EMBL - Bork Group |
PMID:16115313 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-21162, biotools:g2d | http://www.bork.embl-heidelberg.de/g2d/, http://www.ogic.ca/projects/g2d_2/, https://bio.tools/g2d | SCR_008190 | G2D - Candidate Genes to Inherited Diseases, Genes2Diseases | 2026-08-03 09:33:55 | 2 | |||||
|
UniProtKB Resource Report Resource Website 5000+ mentions |
UniProtKB (RRID:SCR_004426) | data repository, data or information resource, database, storage service resource, service resource | Central repository for collection of functional information on proteins, with accurate and consistent annotation. In addition to capturing core data mandatory for each UniProtKB entry (mainly, the amino acid sequence, protein name or description, taxonomic data and citation information), as much annotation information as possible is added. This includes widely accepted biological ontologies, classifications and cross-references, and experimental and computational data. The UniProt Knowledgebase consists of two sections, UniProtKB/Swiss-Prot and UniProtKB/TrEMBL. UniProtKB/Swiss-Prot (reviewed) is a high quality manually annotated and non-redundant protein sequence database which brings together experimental results, computed features, and scientific conclusions. UniProtKB/TrEMBL (unreviewed) contains protein sequences associated with computationally generated annotation and large-scale functional characterization that await full manual annotation. Users may browse by taxonomy, keyword, gene ontology, enzyme class or pathway. | protein, annotation, amino acid sequence, taxonomy, proteome |
uses: UniportKB is used by: NIF Data Federation is used by: PINT is recommended by: NIDDK Information Network (dkNET) is recommended by: National Library of Medicine is related to: ESTHER is related to: PIRSF is related to: AmiGO is related to: UniSave is related to: ProRepeat is related to: UniProt Chordata protein annotation program is related to: neXtProt is related to: TopFIND is related to: UniPathway is related to: NCBI Protein Database is related to: Biomine is related to: Gene Ontology is related to: UniProt DAS is related to: FunTree is related to: ConceptWiki is related to: InterProScan is related to: UniProtKB/Swiss-Prot is related to: FuzDrop has parent organization: UniProt is parent organization of: UniProtKB Keywords is parent organization of: UniProtKB Subcellular Locations works with: PremierBiosoft Proteo IQ Software works with: Cello2Go works with: UniprotR works with: Kinase Associated Neural Phospho Signaling |
PMID:15888679 PMID:18287689 |
Available to the research community, The community can contribute to this resource | r3d100011521, nlx_53981 | https://doi.org/10.17616/R3NK9Z | SCR_004426 | UniProtKB, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, UniProt Knowledgebase | 2026-08-03 09:32:26 | 6654 | ||||||
|
DIANA-mirPath Resource Report Resource Website 100+ mentions |
DIANA-mirPath (RRID:SCR_017354) | production service resource, data analysis service, web service, analysis service resource, data access protocol, service resource, software resource | Web tool for integrating human and mouse microRNAs in pathways.Pathway analysis web-server, providing statistics, while being able to accommodate advanced pipelines. Web server for assessment of miRNA regulatory roles and identification of controlled pathways. Supports all analyses for KEGG molecular pathways and Gene Ontology (GO) in seven species (Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Caenorhabditis elegans, Gallus gallus and Danio rerio).DIANA miRPath v.2.0 includes investigating combinatorial effect of microRNAs in pathways.DIANA-miRPath v3.0 includes deciphering microRNA function with experimental support., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Pathway, analysis, statistics, assessment, miRNA, identify, regulatory, role, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University of Thessaly; Thessaly; Greece is provided by: DIANA Tools works with: KEGG works with: Gene Ontology |
European Social Fund ; John S. Latsis Public Benefit Foundation ; Development Grants For Research Institutions – KRIPIS ; General Secretariat for Research and Technology ; Ministry of Education ; Greece ; European Regional Development Fund |
PMID:25977294 PMID:19435746 PMID:22649059 |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_017495, biotools:diana-mirpath | http://diana.imis.athena-innovation.gr/DianaTools/, http://www.microrna.gr/miRPathv3, https://bio.tools/diana-mirpath | http://www.microrna.gr/miRPathv2 | SCR_017354 | miRPath, miRPathv3, miRPathv2, DIANA-miRPath v2.0, DIANA-miRPath v3.0 | 2026-08-03 09:36:36 | 366 | ||||
|
LIPID MAPS Proteome Database Resource Report Resource Website 1+ mentions |
LIPID MAPS Proteome Database (RRID:SCR_003062) | LMPD | data or information resource, database | Database of lipid related proteins representing human and mouse proteins involved in lipid metabolism. Collection of lipid related genes and proteins contains data for genes and proteins from Homo sapiens, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae, Caenorhabditis elegans, Escherichia coli, Macaca mulata, Drosophila melanogaster, Arabidopsis thaliana and Danio rerio. | gene, protein, lipid, metabolism, metabolomics |
uses: Gene Ontology uses: KEGG uses: UniProt uses: Entrez Gene uses: ENZYME has parent organization: LIPID Metabolites And Pathways Strategy |
NIGMS | PMID:16381922 | Free, Freely available | nif-0000-03085 | http://www.lipidmaps.org/data/proteome/index.cgi | SCR_003062 | LIPID MAPS Proteome Database (LMPD) | 2026-08-03 09:32:09 | 3 | ||||
|
Integrated Molecular Interaction Database Resource Report Resource Website 1+ mentions |
Integrated Molecular Interaction Database (RRID:SCR_003546) | IMID | data or information resource, database | Database for molecular interaction information integrated with various other bio-entity information, including pathways, diseases, gene ontology (GO) terms, species and molecular types. The information is obtained from several manually curated databases and automatic extraction from literature. There are protein-protein interaction, gene/protein regulation and protein-small molecule interaction information stored in the database. The interaction information is linked with relevant GO terms, pathway, disease and species names. Interactions are also linked to the PubMed IDs of the corresponding abstracts the interactions were obtained from. Manually curated molecular interaction information was obtained from BioGRID, IntAct, NCBI Gene, and STITCH database. Pathway related information was obtained from KEGG database, Pathway Interaction database and Reactome. Disease information was obtained from PharmGKB and KEGG database. Gene ontology terms and related information was obtained from Gene Ontology database and GOA database. | pathway, disease, gene ontology, specie, interaction, molecular, protein-protein interaction, gene/protein regulation, protein-small molecule interaction, gene, protein, regulation |
is related to: Gene Ontology is related to: Entrez Gene is related to: Pathway Commons is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: IntAct is related to: Search Tool for Interactions of Chemicals is related to: KEGG is related to: Pathway Interaction Database is related to: Reactome is related to: PharmGKB has parent organization: Florida State University; Florida; USA |
PMID:22238258 | nlx_157667 | SCR_003546 | 2026-08-03 09:32:10 | 1 | ||||||||
|
Cotton EST Database Resource Report Resource Website 10+ mentions |
Cotton EST Database (RRID:SCR_003301) | Cotton EST Database | data or information resource, database | Database platform for cotton expressed sequence tag (EST)-related information, covering assembled contigs, function annotation, analysis of GO and KEGG, SNP, miRNA, SSR-related marker information. | expressed sequence tag, contig, indel mutant, single nucleotide polymorphism, transcription factor, protein kinase, gene, mirna, blast, est-simple sequence repeat, simple sequence repeat, pathway, function |
is related to: Gene Ontology is related to: KEGG has parent organization: East Carolina University; Carolina; USA |
PMID:22087239 | THIS RESOURCE IS NO LONGER IN SERVICE | r3d100011232 | https://doi.org/10.17616/R3X63C | http://www.leonxie.com/ | SCR_003301 | 2026-08-03 09:32:14 | 10 | |||||
|
Babelomics Resource Report Resource Website 100+ mentions |
Babelomics (RRID:SCR_002969) | Babelomics | data analysis service, service resource, analysis service resource, production service resource | An integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Version 4 of Babelomics integrates primary (normalization, calls, etc.) and secondary (signatures, predictors, associations, TDTs, clustering, etc.) analysis tools within an environment that allows relating genomic data and/or interpreting them by means of different functional enrichment or gene set methods. Such interpretation is made not only using functional definitions (GO, KEGG, Biocarta, etc.) but also regulatory information (from Transfac, Jaspar, etc.) and other levels of regulation such as miRNA-mediated interference, protein-protein interactions, text-mining module definitions and the possibility of producing de novo annotations through the Blast2GO system . Babelomics has been extensively re-engineered and now it includes the use of web services and Web 2.0 technology features, a new user interface with persistent sessions and a new extended database of gene identifiers. In this release GEPAS and Babelomics have integrated into a unique web application with many new features and improvements: * Data input: import and quality control for the most common microarray formats * Normalization and base calling: for the most common expression, tiling and SNP microarrays (Affymetrix and Agilent). * Transcriptomics: diverse analysis options that include well established as well as novel algorithms for normalization, gene selection, class prediction, clustering and time-series analysis. * Genotyping: stratification analysis, association, TDT. * Functional profiling: functional enrichment and gene set enrichment analysis with functional terms (GO, KEGG, Biocarta, etc.), regulatory (Transfac, Jaspar, miRNAs, etc.), text-mining, derived bioentities, protein-protein interaction analysis. * Integrative analysis: Different variables can be related to each other (e.g. gene expression to gnomic copy number) and the results subjected to functional analysis. Platform: Online tool | platform, analysis, transcriptomics, proteomics, genomics, normalization, clustering, gene, mirna, protein, interaction, text mining, genotyping, bioentity, functional profiling, statistical analysis, functional annotation, regulatory motif, microarray, fatigo, biclustering, networkminer, gepas, gene expression, FASEB list |
is listed by: OMICtools is listed by: Gene Ontology Tools is related to: Gene Ontology is related to: BioCarta Pathways is related to: KEGG is related to: TRANSFAC is related to: JASPAR has parent organization: CIPF Bioinformatics and Genomics Department |
Spanish Ministry of Science and Innovation BIO2008-04212; Spanish Ministry of Science and Innovation CEN-2008-1002; Red Temtica de Investigacion Cooperativa en Cancer RD06/0020/1019; Instituto de Salud Carlos III |
PMID:20478823 PMID:18515841 PMID:16845052 PMID:14990455 PMID:15980512 PMID:17478504 |
Free for academic use, Account required | OMICS_00748, nif-0000-30144 | http://www.fatigo.org/, http://www.gepas.org/, http://babelomics3.bioinfo.cipf.es | http://www.babelomics.org | SCR_002969 | Babelomics 4: Gene Expression and Functional Profiling Analysis Suite, Babelomics 4 | 2026-08-03 09:32:06 | 136 | |||
|
biomaRt Resource Report Resource Website 1000+ mentions |
biomaRt (RRID:SCR_019214) | software resource, data processing software, software application, data analysis software | Software package that integrates BioMart data resources with data analysis software in Bioconductor. Can annotate range of gene or gene product identifiers including Entrez Gene and Affymetrix probe identifiers with information such as gene symbol, chromosomal coordinates, Gene Ontology and OMIM annotation. Enables retrieval of genomic sequences and single nucleotide polymorphism information, which can be used in data analysis. | BioMart databases, Bioconductor, data analysis, BioMart data integration, gene annotation, gene product identifiers annotation, gene symbol retrival, chromosomal coordinates retrival, genomic sequence retrival, nucleotide polimorphism information, , bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: BioMart Project is related to: BioMart MartView is related to: Entrez Gene is related to: Affymetrix is related to: Gene Ontology is related to: OMIM is related to: Affymetrix |
PMID:16082012 | Free, Available for download, Freely available | biotools:biomart | https://bio.tools/biomart | SCR_019214 | biomaRt v 2.42.1 | 2026-08-03 09:37:13 | 2638 | ||||||
|
GeneCruiser Resource Report Resource Website 1+ mentions |
GeneCruiser (RRID:SCR_003153) | GeneCruiser | web service, data access protocol, service resource, software resource | A web service and web application for the annotation of microarray data providing integrated access to genomic information freely available from public data sources. | gene, genetic variation, probe, variation, annotation |
is listed by: OMICtools is related to: Gene Ontology has parent organization: Broad Institute |
PMID:16030072 | Free, Freely available | OMICS_00760 | https://www.broadinstitute.org/publications/broad3691 | SCR_003153 | 2026-08-03 09:32:13 | 4 | ||||||
|
BioPerl Resource Report Resource Website 100+ mentions |
BioPerl (RRID:SCR_002989) | BioPerl | software toolkit, wiki, narrative resource, source code, software repository, data or information resource, software resource | BioPerl is a community effort to produce Perl code which is useful in biology. This toolkit of perl modules is useful in building bioinformatics solutions in Perl. It is built in an object-oriented manner so that many modules depend on each other to achieve a task. The collection of modules in the bioperl-live repository consist of the core of the functionality of bioperl. Additionally auxiliary modules for creating graphical interfaces (bioperl-gui), persistent storage in RDMBS (bioperl-db), running and parsing the results from hundreds of bioinformatics applications (Run package), software to automate bioinformatic analyses (bioperl-pipeline) are all available as Git modules in our repository. The BioPerl toolkit provides a library of hundreds of routines for processing sequence, annotation, alignment, and sequence analysis reports. It often serves as a bridge between different computational biology applications assisting the user to construct analysis pipelines. This chapter illustrates how BioPerl facilitates tasks such as writing scripts summarizing information from BLAST reports or extracting key annotation details from a GenBank sequence record. BioPerl includes modules written by Sohel Merchant of the GO Consortium for parsing and manipulating OBO ontologies. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | perl, biology, ontology, library, sequence, analysis, computational, application, pipeline, bioinformatics, sequence, annotation, module, life science, python, java, genome, software library, parse, manipulate, bio.tools |
is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is listed by: OMICtools is listed by: SoftCite is related to: Gene Ontology is related to: OBO has parent organization: Duke University; North Carolina; USA has parent organization: European Bioinformatics Institute is required by: RelocaTE |
NIGMS T32 GM07754-22; NHGRI K22 HG00056; NHGRI K22 HG-00064-01; NHGRI HG00739; NHGRI P41HG02223 |
PMID:12368254 DOI:10.1101/gr.361602 |
Free, Available for download, Freely available | OMICS_04849, nif-0000-30188, biotools:bioperl | https://bio.tools/bioperl, https://sources.debian.org/src/bioperl/ | SCR_002989 | 2026-08-03 09:32:10 | 402 | |||||
|
PLANTTFDB Resource Report Resource Website 1000+ mentions |
PLANTTFDB (RRID:SCR_003362) | PlantTFDB | production service resource, data analysis service, service resource, database, analysis service resource, data or information resource | Comprehensive plant transcription factor database. Interface to allow users to search the database by IDs or free texts, to make sequence similarity search against TFs of all or individual species, and to download TF sequences for local analysis.PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors | transcription factor, expression, regulation, interaction, conserved element, phenotype, function, evolution, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: Database of Poplar Transcription Factors is related to: Plant Ontology has parent organization: Peking University; Beijing; China |
China 863 ; China 973 ; NSFC ; China NSFC |
PMID:24174544 PMID:17933783 PMID:21097470 |
Free, Available for download, Freely available | nif-0000-03311, biotools:planttfdb_2.0, OMICS_00560, r3d100010137 | https://bio.tools/planttfdb_2.0, https://doi.org/10.17616/R3JG6V | http://planttfdb.cbi.pku.edu.cn | SCR_003362 | , PlantTFDB 2.0, Plant Transcription Factor Database | 2026-08-03 09:32:14 | 1109 | |||
|
Physico-Chemical Process Resource Report Resource Website |
Physico-Chemical Process (RRID:SCR_003530) | REX | controlled vocabulary, data or information resource, ontology | An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time. It includes both microscopic processes (involving molecular entities or subatomic particles) and macroscopic processes. Some biochemical processes from Gene Ontology (GO Biological process) can be described as instances of REX. | obo, physico-chemical process, physico-chemical, microscopic process, molecular entity, subatomic particle, macroscopic process, biochemical process |
is listed by: BioPortal is listed by: OBO is related to: Gene Ontology has parent organization: CHEBI |
nlx_157639 | http://purl.bioontology.org/ontology/MO, ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/rex.obo, http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=REX | http://www.ebi.ac.uk/~kirill/REX/ | SCR_003530 | Physico-Chemical Process (REX) | 2026-08-03 09:32:10 | 0 | ||||||
|
GOCat Resource Report Resource Website 1+ mentions |
GOCat (RRID:SCR_003608) | GOCat | production service resource, data analysis service, analysis service resource, service resource, software resource | Software tool that uses a machine learning (ML) approach to classify text, based on the Gene Ontology. It relies on a k-Nearest Neighbours algorithm, a simple algorithm which assigns to a new text the categories that are the most prevalent among the k most similar instances contained in the knowledge base. The ML classifier operates in two steps and combines two components. First, a related article search engine retrieves instances (i.e. abstracts) in the knowledge base that are the most similar to the input text (its nearest neighbours); second, a score computer infers the functional profile from the k most similar instances. | machine learning, classification |
is related to: Gene Ontology has parent organization: University of Geneva; Geneva; Switzerland |
PMID:23842461 | nlx_157764 | SCR_003608 | GOCat the Gene Ontology Categorizer, GOCat - the Gene Ontology Categorizer | 2026-08-03 09:32:12 | 2 | |||||||
|
StRAnGER Resource Report Resource Website 10+ mentions |
StRAnGER (RRID:SCR_004247) | StRAnGER | software resource, data processing software, software application, data analysis software | StRAnGER (Statistical Ranking of ANotated Genomic Experimental Results) is a web application for the automated statistical analysis of annotated gene profiling experiments, exploiting controlled biological vocabularies, like the Gene Ontology or the KEGG pathways terms. Starting from annotated lists of differentially expressed genes StRAnGER repartitions and reorders the initial distribution of terms to define a new distribution of elements where each element pools terms holding the same enrichment score. The elements are then prioritized according to StRAnGER''''s algorithm and, by applying bootstrapping techniques, a corrected measure of the statistical significance of these elements is derived, enabling the selection of terms mapped to these elements, unambiguously associated with respective significant gene sets. Besides their high statistical score, another selection criterion for the terms is the number of their members, something that incurs a biological prioritization in line with a Systems Biology context. Platform: Online tool | controlled vocabulary, functional analysis, genomics, annotation, visualization, statistical analysis, term enrichment, ontology or annotation visualization |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: National Hellenic Research Foundation |
PMID:21293737 | Free for academic use | nlx_25932 | SCR_004247 | Statistical Ranking of ANotated Genomic Experimental Results | 2026-08-03 09:32:23 | 18 | ||||||
|
Neural-Immune Gene Ontology Resource Report Resource Website 1+ mentions |
Neural-Immune Gene Ontology (RRID:SCR_004120) | NIGO | controlled vocabulary, data or information resource, ontology | Ontology that is a subset of GO directed for neurological and immunological systems. It was created by clipping those GO terms that are not associated to any gene in human, rat and mouse, and by clipping terms not found to be relevant to the neural and/or immune domains. | obo |
is listed by: BioPortal is related to: Gene Ontology |
nlx_157506 | SCR_004120 | 2026-08-03 09:32:22 | 1 | |||||||||
|
ConceptWiki Resource Report Resource Website 1+ mentions |
ConceptWiki (RRID:SCR_006362) | ConceptWiki | narrative resource, people resource, data or information resource, wiki | A community owned repository of concepts used to define all concepts unambiguously. Users can edit and add their own concepts to the wiki. | wiki, community, concept, unambiguous, repository |
is used by: Open PHACTS is related to: Gene Ontology is related to: Unified Medical Language System is related to: UniProtKB |
Public, The community can contribute to this resource | nlx_152103 | http://www.conceptwiki.org/index.php/Main%20Page | SCR_006362 | 2026-08-03 09:32:59 | 3 | |||||||
|
InterSpecies Analysing Application using Containers Resource Report Resource Website 10+ mentions |
InterSpecies Analysing Application using Containers (RRID:SCR_006243) | ISAAC | production service resource, data analysis service, analysis service resource, service resource, software resource | Web based tool to enable the analysis of sets of genes, transcripts and proteins under different biological viewpoints and to interactively modify these sets at any point of the analysis. Detailed history and snapshot information allows tracing each action. One can switch back to previous states and perform new analyses. Sets can be viewed in the context of genomes, protein functions, protein interactions, pathways, regulation, diseases and drugs. Additionally, users can switch between species with an automatic, orthology based translation of existing gene sets. Sets as well as results of analyses can be exchanged between members of groups. | protein function, protein interaction, pathway, mirna, disease, drug, gene, genome, transcript, protein, regulation |
is listed by: OMICtools is related to: Gene Ontology has parent organization: University of Wurzburg; Bavaria; Germany |
PMID:24428905 | OMICS_02237 | SCR_006243 | ISAAC (Interspecies Analysing Application using Containers), ISAAC - InterSpecies Analysing Application using Containers, Interspecies Analysing Application using Containers - ISAAC | 2026-08-03 09:32:57 | 35 | |||||||
|
ErmineJ Resource Report Resource Website 50+ mentions |
ErmineJ (RRID:SCR_006450) | ermineJ | software resource, data processing software, software application, data analysis software | Data analysis software for gene sets in expression microarray data or other genome-wide data that results in rankings of genes. A typical goal is to determine whether particular biological pathways are doing something interesting in the data. The software is designed to be used by biologists with little or no informatics background. A command-line interface is available for users who wish to script the use of ermineJ. Major features include: * Implementation of multiple methods for gene set analysis: ** Over-representation analysis ** A resampling-based method that uses gene scores ** A rank-based method that uses gene scores ** A resampling-based method that uses correlation between gene expression profiles (a type of cluster-enrichment analysis). * Gene sets receive statistical scores (p-values), and multiple test correction is supported. * Support of the Gene Ontology terminology; users can choose which aspects to analyze. * User files use simple text formats. * Users can modify gene sets or create new ones. * The results can be visualized within the software. * It is simple to compare multiple analyses of the same data set with different settings. * User-definable hyperlinks are provided to external sites to allow more efficient browsing of the results. * For programmers, there is a command line interface as well as a simple application programming interface that can be used to plug ermineJ functionality into your own code Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | microarray, gene ontology, analysis, high-throughput, gene, gene expression, statistical analysis, term enrichment, genome |
is listed by: Gene Ontology Tools is related to: Gene Ontology has parent organization: University of British Columbia; British Columbia; Canada has parent organization: Columbia University; New York; USA |
PMID:16280084 | Free for academic use | nif-0000-07758 | SCR_006450 | ermineJ: Gene Ontology analysis for high-throughput data | 2026-08-03 09:33:04 | 50 | ||||||
|
Debian Resource Report Resource Website 50+ mentions |
Debian (RRID:SCR_006638) | Debian | database, source code, software repository, data or information resource, software resource | Debian is Linux distribution composed of free and open source software, developed by community supported Debian Project, which was established by Ian Murdock on August 16, 1993.Debian comes with over 59000 packages (precompiled software that is bundled up in nice format for easy installation on your machine), package manager (APT), and other utilities that make it possible to manage thousands of packages on thousands of computers as easily as installing single application. | operating system, software package, FASEB list |
lists: GUARDD lists: FACS lists: SNAVI lists: Fusion Analyser lists: GEOquery lists: MIMOSA lists: RNAcontext lists: AffyRNADegradation lists: Patchwork lists: GraBCas lists: GENIE3 lists: MODENT - A Tool For Reconstructing Gene Regulatory Networks lists: Megraft lists: PeptideProphet lists: VARiD lists: Flicker lists: ARACHNE lists: Quant lists: riboPicker lists: cn.FARMS lists: ProteinProphet lists: dbSTS lists: flowPeaks lists: SODOCK lists: PEPPER lists: POPBAM lists: Micro-Analyzer lists: MuTect lists: Mfuzz lists: PGS lists: TAPyR lists: ContEst lists: FPSAC lists: FlipFlop lists: SRMA lists: Pindel lists: PhenoFam lists: DSRC lists: SOAP lists: TriageTools lists: StringTie lists: SplitSeek lists: BLASR lists: Bowtie lists: Barrnap lists: MUSCLE lists: GimmeMotifs lists: massiR lists: CUDA-EC lists: Illuminator lists: SplicePlot lists: SLOPE lists: PARalyzer lists: VAAL lists: BreakSeq lists: ProGlycProt lists: OmicsOffice for NGS SeqSolve lists: TileQC lists: NGSUtils lists: QUAST lists: GenomicTools lists: piCALL lists: SNPchip lists: TALLYMER lists: SABER lists: wateRmelon lists: QualiMap lists: BFCounter lists: ADMIXTURE lists: OLIN lists: DEXUS lists: limmaGUI lists: KAnalyze lists: oneChannelGUI lists: BeadDataPackR lists: affylmGUI lists: SAMBLASTER lists: PyLOH lists: fRMA lists: CYCLE lists: FARMS lists: MACAT lists: GlyProt lists: YinOYang lists: Sequedex lists: DictyOGlyc lists: ToppCluster lists: Biocatalogue - The Life Science Web Services Registry lists: ProbRNA lists: HAPLOPAINTER lists: Chilibot: Gene and Protein relationships from MEDLINE lists: GERMLINE lists: FACTA+. lists: CisGenome lists: asSeq lists: unifiedWMWqPCR lists: HOMOZYGOSITYMAPPER lists: Prediction of Amyloid Structure Aggregation lists: InterMine lists: TANGO lists: CQN lists: MEME Suite - Motif-based sequence analysis tools lists: pRESTO lists: S-MART lists: PhosphoSitePlus: Protein Modification Site lists: myExperiment lists: DINDEL lists: Skylign lists: PEDIGRAPH lists: ADaCGH2 lists: CCAT lists: AnimalTFDB lists: TEMP lists: CanSNPer lists: Candida Genome Database lists: SamSPECTRAL lists: InteroPorc lists: MetaBase lists: Pecan lists: cisRED: cis-regulatory element lists: AffyPipe lists: SHORTY lists: BISC lists: Pathway Commons lists: Cake lists: SNVer lists: WebGeSTer DB lists: FlyFactorSurvey lists: ASPGD lists: TcoF lists: cpnDB: A Chaperonin Database lists: ZOOM lists: CAMERA - Collection of annotation related methods for mass spectrometry data lists: BEETL-fastq lists: NGSrich lists: ShotGun lists: Iterative Signature Algorithm lists: SBARS lists: SNPAAMapper lists: Autophagy Database lists: RUbioSeq lists: COSMIC - Catalogue Of Somatic Mutations In Cancer lists: EchoBASE lists: QualitySNPng lists: Pathview lists: pymzML lists: RopeBWT2 lists: ExomeDepth lists: NetPathMiner lists: leeHom lists: PurBayes lists: libCSAM lists: SuperPred: Drug classification and target prediction lists: HGNC lists: Coding Potential Calculator lists: T3DB lists: CPTRA lists: BioNumbers lists: GATE lists: ProRata lists: GreenPhylDB lists: BREAKDANCER lists: GeneFisher lists: tweeDEseq lists: HYDEN lists: Eukaryotic Linear Motif lists: Primer3Plus lists: MethylAid lists: Triplex lists: Distant Regulatory Elements lists: hot scan lists: MFEprimer lists: Proteome Analyst Specialized Subcellular Localization Server lists: mrsFAST lists: BioJS lists: FastSNP lists: Gene Set Enrichment Analysis lists: Pipeliner lists: ms lims lists: GenePattern lists: rBiopaxParser lists: QDNAseq lists: MutDB lists: Piano lists: NovelSeq lists: MAGE-TAB lists: Database of Interacting Proteins (DIP) lists: Weighted Gene Co-expression Network Analysis lists: Blood Group Antigen Gene Mutation Database lists: drFAST lists: pairheatmap lists: MiST - Microbial Signal Transduction database lists: AltAnalyze - Alternative Splicing Analysis Tool lists: SplicingCompass lists: deFuse lists: Assembly Based ReAligner lists: ggbio lists: miR-PREFeR lists: ALDEx2 lists: HTqPCR lists: NanoStringNorm lists: T-profiler lists: Snakemake lists: jmzTab lists: MIPgen lists: Bpipe lists: PoPoolation lists: L-Measure lists: MultiPhen lists: PheWAS R Package lists: InsertionMapper lists: Quantitative Enrichment of Sequence Tags lists: INMEX lists: Segway - a way to segment the genome lists: SeWeR - SEquence analysis using WEb Resources lists: TagDust lists: BSRD lists: DER Finder lists: Stem Cell Discovery Engine lists: Kdetrees lists: Tree and reticulogram REConstruction lists: BioPig lists: NCBI BioSystems Database lists: Distributed String Mining Framework lists: NEWT lists: PILGRM lists: Selectome: a Database of Positive Selection lists: SVMerge lists: Parseq lists: SVseq lists: Small Molecule Pathway Database lists: miRNAKey lists: DELLY lists: Apo and Holo structures DataBase lists: BioSample Database at EBI lists: MetaPhyler lists: MG-RAST lists: SLIQ lists: SOPRA lists: Information Hyperlinked Over Proteins lists: AmphoraNet lists: SINA lists: SSPACE lists: Percolator: Semi-supervised learning for peptide identification from shotgun proteomics datasets lists: STING Report lists: G-BLASTN lists: RNA-eXpress lists: MethPipe lists: SoyBase lists: Strelka2 lists: RUM lists: SPOT - Biological prioritization after a SNP association study lists: VFS lists: PHAge Search Tool lists: MLTreeMap lists: SEECER lists: GeneTalk lists: ERANGE lists: rQuant lists: NCBO Annotator lists: ShoRAH lists: Yabi lists: ORMAN lists: FusionMap lists: CoPub lists: Scripture lists: SolexaQA lists: Kismeth lists: EMAGE Gene Expression Database lists: SAMStat lists: Knime4Bio lists: Bis-SNP lists: GobyWeb lists: Jellyfish lists: PRINSEQ lists: PASS lists: GSNAP lists: SOAPaligner/soap2 lists: MethylViewer lists: READSCAN lists: DistMap lists: MicrobesOnline lists: mrFAST lists: FLASH lists: TIGRFAMS lists: TMA Navigator lists: Bambino lists: TreQ lists: SeqMap lists: SeqTrace lists: TRANSFAC lists: GoFish lists: MethylomeDB lists: CLIPZ lists: SerbGO lists: ToppGene Suite lists: ngsTools lists: PePr lists: DMRforPairs lists: CharProtDB: Characterized Protein Database lists: Expression Profiler lists: SNPsandGO lists: GoSurfer lists: WEGO - Web Gene Ontology Annotation Plot lists: SOURCE lists: Stampy lists: DiseaseMeth lists: BLESS lists: GraphProt lists: GoPubMed lists: ccPDB - Compilation and Creation of datasets from PDB lists: Europe PubMed Central lists: Dr.VIS - Human Disease-Related Viral Integration Sites lists: DOMMINO - Database Of MacroMolecular INteractiOns lists: DBETH - Database for Bacterial ExoToxins for Humans lists: VirHostNet: Virus-Host Network lists: GWASdb lists: HFV Database lists: HotRegion - A Database of Cooperative Hotspots lists: eQuilibrator lists: FunTree lists: Cascade lists: 959 Nematode Genomes lists: ICEberg lists: IndelFR - Indel Flanking Region Database lists: IDEAL - Intrinsically Disordered proteins with Extensive Annotations and Literature lists: ProRepeat lists: NRG-CING lists: InterEvol database lists: MMMDB - Mouse Multiple tissue Metabolome DataBase lists: Newtomics lists: MIPModDB lists: DistiLD - Diseases and Traits in LD lists: Polbase lists: UMD-BRCA1/ BRCA2 databases lists: ScerTF lists: VIRsiRNAdb lists: ProPortal lists: OGEE - Online GEne Essentiality database lists: RecountDB lists: PRED-GPCR lists: RNA CoSSMos lists: PRED-SIGNAL lists: SNPedia lists: SpliceDisease lists: HMM-TM lists: deepSNV lists: OMPdb lists: PRED-LIPO lists: VICUNA lists: Predictive Networks lists: COEUS lists: GeneTrail lists: epigenomix lists: ADGO lists: SRAdb lists: QCGWAS lists: Flycircuit lists: MouseBook lists: Immune Epitope Database and Analysis Resource (IEDB) lists: SitEx lists: GOEAST - Gene Ontology Enrichment Analysis Software Toolkit lists: MSIsensor lists: TSSer lists: ATRHUNTER lists: Phytozome lists: Decombinator lists: ViralZone lists: COLT-Cancer lists: Gene Expression Database lists: BEDTools lists: waviCGH lists: Pseudomonas Genome Database lists: BIGpre lists: MyHits lists: CAPS Database lists: SpliceTrap lists: EagleView lists: IMGT/LIGM-DB lists: RIKEN integrated database of mammals lists: COHCAP lists: DARC - Database for Aligned Ribosomal Complexes lists: canSAR lists: GWAMA lists: AutismKB lists: zfishbook lists: PomBase lists: Myrna lists: PLEXdb - Plant Expression Database lists: RamiGO lists: PhenoM - Phenomics of yeast Mutants lists: IMGT/GENE-DB lists: HIstome: The Histone Infobase lists: SCOP: Structural Classification of Proteins lists: CuticleDB lists: agriGO lists: Expression Database in 4D lists: ESEfinder 3.0 lists: TriTrypDB lists: VIDA lists: Database of Arabidopsis Transcription Factors lists: Atlas of Genetics and Cytogenetics in Oncology and Haematology lists: AgBase lists: Hyper Cell Line Database lists: Midbody, Centrosome and Kinetochore lists: Chromosome 7 Annotation Project lists: MfunGD - MIPS Mouse Functional Genome Database lists: Taipan lists: VISTA Browser lists: T1DBase lists: lobSTR lists: VISTA Enhancer Browser lists: MEROPS lists: Gene Array Analyzer lists: Network Analysis, Visualization and Graphing TORonto lists: Candidate Genes to Inherited Diseases lists: Single Nucleotide Polymorphism Spectral Decomposition (SNPSpD) lists: eTBlast lists: hiPathDB - human integrated Pathway DB with facile visualization lists: MuSiC lists: miRNEST lists: QuasiRecomb lists: neXtProt lists: DNAtraffic lists: BeeBase lists: NetOGlyc lists: GenoTan lists: GMAP lists: LegumeIP lists: SeqBuster lists: elastix lists: iMir lists: WEBLOGO lists: MaCH-Admix lists: Pathema lists: SNPinfo Web Server lists: MOSCPHASER lists: NEBcutter lists: Atlas2 lists: FGDP lists: Velvet lists: HomSI lists: MicroSNiPer lists: MIRA lists: ALLPATHS-LG lists: CUPSAT lists: SVDetect lists: omiRas lists: CopySeq lists: MutSig lists: HapFABIA lists: DIANA-LncBase lists: MutationTaster lists: HMCan lists: Geneious lists: kmer-SVM lists: SICER lists: ZINBA lists: Pedimap lists: MAnorm lists: PlantTFcat lists: MethMarker lists: NPS lists: PeakRanger lists: SEAL lists: OligoArray lists: PSAR-Align lists: CEQer lists: CloudBurst lists: nucleR lists: RACE lists: Asterias lists: PatMaN lists: RobiNA lists: LitInspector lists: Btrim lists: ArrayAnalysis.org lists: CANGS lists: GeneStitch lists: ProDesign lists: JiffyNet lists: AlienTrimmer lists: GenoREAD lists: HSLPred lists: CancerResource lists: FABIA lists: PlnTFDB lists: easyRNASeq lists: OBI-Warp lists: PREDDIMER lists: ECHO lists: ICPL ESIQuant lists: PRIDE Converter 2 lists: SlideSort-BPR lists: COBRApy lists: MFPaQ lists: TopHat-Fusion lists: miRPlant lists: SNP ratio test lists: compomics-utilities lists: PLEK lists: multiplierz lists: Allim lists: ISDTool lists: NetCoffee lists: MToolBox lists: Scalpel lists: DNaseR lists: LocalAli lists: NAIL lists: iceLogo lists: GPU-Meta-Storms lists: AMS lists: rqubic lists: ANNOVAR lists: A5-miseq lists: PhosphoSiteAnalyzer lists: Cell motility lists: MethylCoder lists: CAZy- Carbohydrate Active Enzyme lists: CPFP lists: GENE-counter lists: PoolHap lists: LOCAS lists: CloudAligner lists: HeurAA lists: Mouse Genome Database lists: MitoBreak lists: PolyPhen: Polymorphism Phenotyping lists: GSA-SNP lists: featureCounts lists: Crossbow lists: CSAR lists: seqMINER lists: BEADS lists: IUPHAR/BPS Guide to Pharmacology lists: QuantiSNP lists: Cube-DB lists: Death Domain database lists: psRNATarget lists: DSAP lists: PlantNATsDB - Plant Natural Antisense Transcripts DataBase lists: GeneSigDB lists: MACS lists: NGSmethDB lists: GENSCAN lists: INCLUSive lists: MINAS - Metal Ions in Nucleic AcidS lists: Composition Profiler lists: NNcon lists: EGSEA lists: SCRATCH lists: Telescoper lists: Buccaneer lists: ProtTest lists: Morpheus lists: KAVIAR lists: DISEASES lists: SPEX2 lists: RAST Server lists: GeneWise lists: Crystallography and NMR System (CNS) lists: FATCAT lists: Membrane Protein Explorer lists: LTR_Finder lists: PALEOMIX lists: TISSUES lists: MetaMapR lists: primers4clades lists: MS-GF+ lists: PLAN2L lists: Off-Spotter lists: ProteomicsDB lists: CHiCAGO lists: SC3 lists: Bio-tradis lists: ApiDB CryptoDB lists: HISAT2 lists: PhyD3 lists: LoRDEC lists: Bamtools lists: ALTER lists: MultiQC lists: TFBS lists: EnrichmentMap lists: Poretools lists: Exonerate lists: 3D-footprint lists: Genesis lists: oligo lists: DISULFIND lists: Fastml lists: mentha lists: Oufti lists: eXpression2Kinases lists: IDEPI - IDentify EPItopes lists: SMAGEXP lists: ProCon - PROteomics CONversion lists: TRANSIT lists: DINIES lists: Splicing Express lists: FluxModeCalculator lists: Lifebit Deploit lists: ngsRelate lists: SARTools lists: OmicsNet lists: SPICE lists: Microscopy Image Browser lists: Thunder STORM lists: clusterProfiler lists: NetworkAnalyst lists: ANOCVA lists: Rsubread lists: Subread lists: ConsensusClusterPlus lists: CIBERSORT lists: FRETBursts lists: CCTOP lists: scran lists: ScaffMatch lists: Heatmapper lists: Goseq lists: PRSice lists: UMI-tools lists: Proovread lists: BinPacker lists: JAMM lists: CentroidFold lists: ComplexHeatmap lists: PatchDock lists: FastProject lists: ExPASy ABCD database lists: Gigwa lists: shinyGEO lists: GeSeq lists: EMBOSSMatcher lists: Geneshot lists: Mousebytes lists: trimAl lists: AmoebaDB lists: STRUCTURE lists: PASTEClassifier lists: NetPhos lists: HiC-Pro lists: SWISS-MODEL lists: Blood Exposome Database lists: HingeProt lists: ChiCMaxima lists: ProtParam Tool lists: GalaxyRefine lists: FlowCal lists: SpydrPick lists: R/qtl2 lists: Roary lists: SIGNOR lists: Protein Interactions Calculator lists: REDIportal lists: MaxAlign lists: Minimap2 lists: PrognoScan lists: GPS-SUMO lists: Signaling Pathways Project lists: ProSA-web lists: GalaxyWEB lists: iTOL lists: EpiModel lists: rVista lists: AlgPred lists: D-GENIES lists: Robetta lists: GOnet lists: E-CRISP lists: STAMP lists: Batch Web CD-Search Tool lists: aroma.light lists: Annotree lists: Database of Secondary Structure Assignments lists: Clustal Omega lists: DESeq lists: discoSnp lists: vcflib lists: Genome BioInformatics Research Lab - gff2ps lists: Primer3 lists: BioPerl lists: Rainbow lists: RNAhybrid lists: Clustal W2 lists: Apollo lists: IgBLAST lists: Ray lists: khmer lists: Stacks lists: Predictions for Entire Proteomes lists: DIALIGN lists: EBSeq lists: Minia lists: SAMtools/BCFtools lists: Artemis: Genome Browser and Annotation Tool lists: NCBI BLAST lists: biobambam lists: VICMpred lists: Staden Package lists: Bowtie 2 lists: RAxML lists: WHAM lists: VarScan lists: Bismark lists: ea-utils lists: HTSeq lists: Vienna RNA lists: Regulatory Sequence Analysis Tools lists: BitSeq lists: COILS: Prediction of Coiled Coil Regions in Proteins lists: HilbertVis lists: BRIG lists: Unipro UGENE lists: GBrowse lists: Sickle lists: AmpliconNoise lists: FreeBayes lists: tRNAscan-SE lists: CD-HIT lists: SSAKE lists: MACH lists: Segemehl lists: BEAST lists: Pscan-ChIP lists: cutadapt lists: Oases lists: CGView lists: SOAPsnp lists: T-Coffee lists: Kalign lists: Circos lists: Trinity lists: Flexbar lists: SIFT lists: ProbCons lists: OpenMS lists: RSEM lists: Glimmer lists: GROMACS lists: CummeRbund lists: edgeR lists: DNAcopy lists: TopHat lists: SortMeRNA lists: LIMMA lists: AMOS lists: Cufflinks lists: Nanopolish lists: GMA lists: Prokka lists: phyloseq lists: SeqPrep lists: precrec lists: Atac lists: PAML lists: KisSplice lists: StoatyDive lists: IMGT-ONTOLOGY lists: KAT lists: SeaView lists: FastTree lists: Crux tandem mass spectrometry analysis software lists: rCASC lists: minet lists: becas lists: tximport lists: globaltest lists: CheckM lists: BLINK lists: mosdepth lists: bwtool lists: dcmqi lists: Pilon lists: ASHLAR lists: metagen lists: COPASI lists: BUSCO lists: bridge lists: TGS-GapCloser lists: NiftyPET lists: Blobtools lists: THESIAS lists: Fcirc lists: chimerascan lists: GLUE lists: SwiftOrtho lists: HaploReg lists: ScanITD lists: andi lists: metahdep lists: ImaGene lists: Jalview lists: MeroX lists: qrqc lists: BioNix lists: MiXCR lists: casper lists: libmgf lists: sleuth lists: imDEV lists: miRDB lists: yaqcaffy lists: NiftyFit lists: mlgt lists: SMARTdenovo lists: HH-suite lists: StatAlign lists: affy lists: shovill lists: Fiji lists: Racon lists: rbsurv lists: quantsmooth lists: tensorflow lists: seqbias lists: ngs.plot lists: bsseq lists: MGnify lists: dyebias lists: h5vc lists: ascat lists: Cuffdiff lists: mitopred lists: OrthoFinder lists: PIRATE lists: Bridger lists: Eoulsan lists: VEnCode lists: eTRIKS lists: fracridge lists: lumi lists: genomation lists: Hippocampome.org lists: SymPy lists: icy lists: GADMA lists: HaTSPiL lists: XL-mHG lists: ropls lists: scanpy lists: MethBase lists: sabre lists: plgem lists: MyGene.info lists: CRISPRcasIdentifier lists: biobakery lists: VETA lists: EpiEstim lists: HyPhy lists: ODAM lists: BISE lists: docker4seq lists: qcmetrics lists: Pavian lists: genehunter-imprinting lists: smashpp lists: NanoSim lists: SimVascular lists: BSA4Yeast lists: minfi lists: TDimpute lists: RepeatScout lists: neuroelectro lists: MRIcron lists: RepeatFiller lists: ShinyLearner lists: CRISPR-ERA lists: CRISPR-P lists: Warp lists: GEMINI lists: MAFFT lists: TransDecoder lists: Phenoscape lists: PhenoMeNal lists: les lists: Laniakea lists: CandiMeth lists: eisa lists: ProP Server lists: ggtree lists: scVelo lists: PathwayMatcher lists: charm lists: Telescope lists: skewer lists: multtest lists: Human Neocortical Neurosolver lists: beadarray lists: BioBERT lists: PlotTwist lists: GraphClust2 lists: METAREP lists: QIIME lists: halSynteny lists: scater lists: Galaxy scater lists: larvalign lists: iontree lists: VAPPER lists: GENCODE lists: Datanator lists: Bio2BEL lists: UALCAN lists: ffpe lists: MCScan lists: VisR lists: Metascape lists: GemSIM lists: EvidenceFinder lists: pepwheel lists: RDXplorer lists: bcbio-nextgen lists: OpenWorm lists: ActiveDriver lists: QuickNII lists: timecourse lists: Bionitio lists: ggplot2 lists: TCW lists: SPM lists: pvac lists: GeneMarkS-T lists: ascend lists: RatMine lists: CRISPRdirect lists: phantompeakqualtools lists: prank lists: refgenie lists: NanoPipe lists: vsn lists: PAFScaff lists: odMLtables lists: biospytial lists: NeuroChaT lists: clustergrammer lists: glycomedb lists: CLIP-Explorer lists: pheatmap lists: EnteroBase lists: GigaSOM.jl lists: bio.tools lists: SPP lists: lapmix lists: EHRtemporalVariability lists: HmtVar lists: SnpHub lists: Online Peri-Event Time Histogram for Open Ephys lists: NMRProcFlow lists: QGIS lists: Flye lists: kallisto lists: clipcrop lists: cn.mops lists: UniCarbKB lists: pickgene lists: PsyGeNET lists: seq-annot lists: PASA lists: ReadqPCR lists: breseq lists: e-Driver lists: sim4cc lists: PhylomeDB lists: fastqz lists: PerM lists: rnaQUAST lists: NCBI BioProject lists: PEMer lists: metabnorm lists: FusionCatcher lists: STAR lists: VCFtools lists: UniCarb-DB lists: NormqPCR lists: SnpEff lists: DecGPU lists: gprege lists: VirusMINT lists: nondetects lists: circlize lists: SAMTOOLS lists: Neuroscience Information Framework lists: Dali Server lists: IRanges lists: dbEST lists: Genomic Ranges lists: eProbalign lists: Cistrome lists: DIANA-mirPath lists: BpForms lists: GenomicFeatures lists: SOAPdenovo lists: BcForms lists: 4See lists: ABNER lists: A Classification of Mobile genetic Elements lists: Addgene lists: BadMedicine lists: ADMIXMAP lists: ADMIXTOOLS lists: ALCHEMY lists: AETIONOMY lists: ABS: A Database of Annotated Regulatory Binding Sites From Orthologous Promoters lists: ALBERT lists: ALOHOMORA lists: Alternate splicing gallery lists: Allele Frequencies in Worldwide Populations lists: AmpliconTagger lists: Molecular Dynamics Workflow (BioKepler) lists: ape lists: Alta-Cyclic lists: Assisted Model Building with Energy Refinement (AMBER) lists: Aroma.affymetrix lists: ANDES lists: ASSOCIATIONVIEWER lists: ArrayMiner lists: ASPEX lists: The Alternatve Splicing Database lists: AutoAssemblyD lists: AutoDock Vina lists: BAIT lists: BamView lists: Avogadro lists: ArrayPipe lists: Athena lists: BLAT lists: BARS lists: BayesEpiModels lists: BatMeth lists: BeetleBase lists: BBSeq lists: naiveBayesCall lists: BarraCUDA lists: BCBtoolkit lists: BioConda lists: BAR lists: BiG-SLiCE lists: SVM based method for predicting beta hairpin structures in proteins lists: betaVAEImputation lists: BiNGO: A Biological Networks Gene Ontology tool lists: Bioinformatics Toolkit lists: BioCarta Pathways lists: Biopieces lists: Bio++ lists: BioPlex lists: BioSimulations lists: BRAIN lists: BOMP: beta-barrel Outer Membrane protein Predictor lists: biomaRt lists: bioSyntax lists: Bionimbus lists: BioSimulators lists: bioRxiv lists: Breakpointer lists: CiLiQuant lists: BSVF lists: BS Seeker lists: Bs-Seeker2 lists: BWA lists: CARD lists: Canu lists: Cell Image Library (CIL) lists: BRB-ArrayTools lists: CATALYST lists: CATH: Protein Structure Classification lists: CAT lists: CEM lists: CASPAR lists: CHEBI lists: ChimeraSlayer lists: CATdb: a Complete Arabidopsis Transcriptome database lists: ChemSpider lists: Chipster lists: CCREL lists: cisTEM lists: circlncRNAnet lists: Centrifuge Classifier lists: Cancer Genome Anatomy Project lists: ChIPMunk lists: Chromas lists: CiteFuse lists: CRCView lists: ChiRA lists: ClinVar lists: ClinTrajAn lists: clustLasso lists: CleanEx lists: Clinotator lists: CNVer lists: ComiR lists: CODEHOP lists: ClustVis lists: Comparative Metatranscriptomics Workflow lists: CMap lists: CorMut lists: CNV-seq lists: Coot lists: CITE-seq-Count lists: CoCo lists: CopyDetective lists: Chromosome Scale Assembler lists: cortex lists: ConDeTri lists: CRISPy-web lists: CONTRA lists: CovalentDock Cloud lists: CUDASW++ lists: COGEME Phytopathogenic Fungi and Oomycete EST Database lists: DANPOS2 lists: DOGMA lists: CorrDrugTumorMSI lists: DAMBE lists: D-EE lists: CoryneRegNet lists: ΔG prediction server lists: DIAMOND lists: CYANA lists: Datasets2Tools lists: DEXSeq lists: DichroWeb lists: NCBI database of Genotypes and Phenotypes (dbGap) lists: DBTSS: Database of Transcriptional Start Sites lists: dbSNP lists: DiffBind lists: DETONATE lists: DiProGB lists: Descriptions of Plant Viruses lists: DIME lists: DicomTypeTranslator lists: CSDeconv lists: Dictyostelium discoideum genome database lists: DSK lists: DGIdb lists: DisProt - Database of Protein Disorder lists: DOMINE: Database of Protein Interactions lists: eDMR lists: ECLIPSE lists: Experimental Design Assistant lists: Dissect lists: Evolutionary Couplings Server lists: Enrichr lists: ensembldb lists: European Genome phenome Archive lists: EBCall lists: Ensembl Genomes lists: EMAN lists: ENIGMA lists: DISENTANGLER lists: Entrez Gene lists: Ensembl lists: eQtlBma lists: EpiGRAPH lists: EpiDISH R package lists: Examl lists: epitopepredict lists: DrivAER lists: Variant Effect Predictor lists: Epigenomics Workflow on Galaxy and Jupyter lists: Eukaryote Genes lists: Evex lists: FateID lists: EXOMEPICKS lists: European Variation Archive (EVA) lists: FANTOM DB lists: Genome Annotation Generator lists: FireDB lists: FGENESH lists: FluoRender lists: FLOSS lists: fineSTRUCTURE lists: FastQC lists: FINDbase Worldwide lists: ExpressYourself lists: fgsea lists: FuncAssociate: The Gene Set Functionator lists: NHLBI Exome Sequencing Project (ESP) lists: FlyBase lists: FlexProt: flexible protein alignment lists: GASV lists: Fugu Genome Project lists: Full-Length cDNA Database lists: FragGeneScan lists: FunRich: Functional Enrichment analysis tool lists: FlowSOM lists: GASSST lists: GeMoMa lists: An Integrated Multiple Structure Visualization and Multiple Sequence Alignment Application lists: GEDIT lists: VBASE2 lists: Genome Database for Rosaceae lists: GenePattern Notebook lists: G-Mo.R-Se lists: FusionHunter lists: Genome Projector lists: GeneCodis lists: GEN3VA lists: GENERECON lists: GEMB lists: GeCo3 lists: Gene3D lists: Genomic Annotation in Livestock for positional candidate LOci lists: Gene Expression Atlas lists: GeneProf lists: Genome Trax lists: Genome Reviews lists: GATK lists: FunCluster lists: GFINDer: Genome Function INtegrated Discoverer lists: GermOnline lists: GeneSeeker lists: Gmove lists: Genometa lists: GensearchNGS lists: HARSH lists: Gibbs Motif Sampler lists: Generic GO Term Mapper lists: Genomedata lists: GMcloser lists: GEO2R lists: Gramene lists: Genome Aggregation Database lists: GoMapMan lists: GEPAT lists: Git lists: GNUMAP lists: Generic GO Term Finder lists: Graph2GO lists: Gene Ontology lists: Gaggle lists: GO2MSIG lists: GRASS lists: Bioinformatic Harvester IV (beta) at Karlsruhe Institute of Technology lists: Genovar lists: HASTE-project lists: H-InvDB lists: Homologous Sequences in Ensembl Animal Genomes lists: Google lists: IMGT/HLA lists: Human Gene Mutation Database lists: GTDB-Tk lists: G protein receptor interaction feature finding instrument lists: HubMed lists: HPEPDOCK Server lists: HUGE - Human Unidentified Gene-Encoded large proteins lists: HAPLOCLUSTERS lists: HiCUP lists: International HapMap Project lists: HiPipe lists: HTR lists: HINT lists: Hybrid-denovo lists: HS-TDT lists: Human Gene Connectome Server lists: HSSP lists: iDASH lists: hyfi: software suite for binding site search lists: HUDSEN lists: IMGT/StatClonotype lists: I-TASSER lists: ImJoy lists: IMEx - The International Molecular Exchange Consortium lists: IMG System lists: HCLUST lists: Human Splicing Finder lists: lme4 lists: Identifiers.org lists: IPD - Immuno Polymorphism Database lists: IntEnz- Integrated relational Enzyme database lists: IBIS: Inferred Biomolecular Interactions Server lists: IMGT - the international ImMunoGeneTics information system lists: Integr8 : Access to complete genomes and proteomes lists: IMGT HighV-QUEST lists: Isaac lists: Interolog/Regulog Database lists: InterProScan lists: IRESite lists: IPI lists: inGAP lists: ISFinder lists: KGGSeq lists: iPiG lists: IsoLasso lists: J-Express lists: JGI Genome Portal lists: IsaCGH lists: lncRNAdb lists: LDSELECT lists: IsoEM lists: Database oDatabase of Predicted Subcellular Localization for Eukaryotic PDB Chainsf Predicted Subcellular Localization for Eukaryotic PDB Chains lists: IMG lists: LTR_FINDER_parallel lists: LAST lists: MBGD - Microbial Genome Database lists: jmzML lists: OntoQuest lists: LOCUSMAP lists: MaizeGDB lists: long-read-tools lists: LRPath lists: Magic lists: LS-SNP/PDB lists: LOCATE: subcellular localization database lists: Mammalian Gene Collection lists: Machado lists: MACiE lists: Maqview lists: LitMiner lists: MAKER lists: MEBS: Multigenomic Entropy-Based Score lists: MapSplice lists: Mascot lists: mapDamage lists: MEGAHIT lists: Metabolomics Workbench lists: Libra lists: ML Repo lists: MARRVEL lists: Maq lists: MentaLiST lists: MB-GAN lists: MetaCyc lists: MAP lists: MeQA lists: Metastats lists: MatrixDB lists: MetAMOS lists: MeRIP-PF lists: MendelIHT.jl lists: metaXplor lists: lsa_slurm lists: MetaCyto lists: UEA sRNA Workbench lists: MetaVelvet lists: MMAPPR lists: MBCluster.Seq lists: MIP Scaffolder lists: MERMAID lists: MobiDB lists: MPDA lists: MaSuRCA lists: MICSA lists: MIRIAM Resources lists: miROrtho: the catalogue of animal microRNA genes lists: NCBI lists: proMODMatcher lists: miRBase lists: MethylExtract lists: SCIPION lists: MPscan lists: mirTools lists: MISA lists: MP3 tool lists: Mspire-Simulator lists: Multi-omics Visualization Platform lists: mrCaNaVaR lists: MoDIL lists: MultiLoc lists: MULTIDISEQ lists: Noncoding RNA database lists: MRFSEQ lists: MizBee lists: Multiple Myeloma survival predictor lists: Mouse Phenome Database (MPD) lists: Nucleic Acid Database lists: Myriads lists: miRpathDB lists: MUMmer lists: mzMatch lists: NeLS lists: NEST Simulator lists: MutPred lists: NEMBASE lists: Open Babel lists: NetMHCpan Server lists: MULTIMAP lists: NCBI Genome Workbench lists: Nephele lists: NCBI Probe lists: Ngmlr lists: Necklace lists: NetNGlyc lists: NucleoFinder lists: NeuroMatic lists: Genotyping lists: NGSView lists: NOrMAL lists: Opera lists: NURD lists: ngLOC lists: NeSSM lists: NanoGalaxy lists: ObjTables lists: nmrML lists: nsSNPAnalyzer lists: OsiriX Medical Imaging Software lists: parSMURF lists: Open Trials lists: Ngs backbone lists: PartiGeneDB lists: Pfam lists: Oncodrive-fm lists: Online Resource for Community Annotation of Eukaryotes lists: PanoramaWeb lists: Omics Data Paper Generator lists: Pathway Tools lists: PDBe - Protein Data Bank in Europe lists: Pash 3.0 lists: Orientations of Proteins in Membranes database lists: Pathbase lists: PEDHUNTER lists: PAZAR lists: Peakzilla lists: PeakAnalyzer lists: Pairwise Conservation Scores - An Algorithm to Identify Conserved K-mers lists: Pedigree-Draw lists: OLego lists: Parliament2 lists: PEDIGREEQUERY lists: PeakSeq lists: PEDPEEL lists: PhaseME lists: PHI-base lists: PHYLIP lists: PDB Finder lists: Phylogeny.fr lists: PRICE lists: PennSeq lists: Illuminating the Druggable Genome lists: Philius lists: Phenotypes and eXposures Toolkit lists: PhyloPat lists: PicTar lists: Eddy Lab Software lists: Protein Information Resource lists: PhyML lists: PhenoMan lists: PeptideAtlas lists: PIRSF lists: Polygenic Pathways lists: PLANTTFDB lists: pNovo+ lists: PLINK/SEQ lists: PEMA lists: pFind Studio: pLink lists: PM4NGS lists: PrimerBank lists: ProSight Lite lists: PolymiRTS lists: Phospho.ELM lists: Plant Co-expression Annotation Resource lists: Rampart lists: Protein Prospector lists: ProteomeXchange lists: PRED-TMBB lists: Proteomics Identifications (PRIDE) lists: PS-Plant Framework lists: ProtChemSI lists: PRADA lists: Pyntacle lists: PubCrawler lists: ProfCom - Profiling of complex functionality lists: PrimerSeq lists: PyBEL lists: PubChem lists: PubGene lists: R/QTLBIM lists: QGene lists: QMSIM lists: QmRLFS-finder lists: PolyPhred lists: QSRA lists: Preseq lists: ReactomePA lists: QuickGO lists: QUMA lists: RAREMETAL lists: REDItools lists: The Human Protein Atlas lists: rSNP Guide lists: PyRosetta lists: RefSeq lists: RaptorX lists: Reaper - Demultiplexing trimming and filtering sequencing data lists: RegulonDB lists: RESID lists: R Project for Statistical Computing lists: Reactome lists: Rdisop lists: RepeatModeler lists: RESCUE-ESE lists: Relate lists: Reptile lists: R-SAP lists: riborex lists: RNA-SeQC lists: QuPath lists: RNA FRABASE - RNA FRAgments search engine and dataBASE lists: RADAR-base lists: RiboTaper lists: SAMMate lists: rna-stability lists: RightField lists: SASGENE lists: RNAplex lists: runBioSimulations lists: ResponseNet lists: SilkDB lists: Scansite lists: Research-tested Intervention Programs (RTIPs) lists: sapFinder lists: SeqtrimNEXT lists: RNA Virus Database lists: SALT lists: SEEK lists: Seqtk lists: REDfly Regulatory Element Database for Drosophilia lists: SAFA Footprinting Software lists: SeqExpress lists: ROMPREV lists: SeqSaw lists: SeqEM lists: SHELX lists: rSeq lists: SHARCGS lists: rnaSPAdes lists: SimSeq lists: SGA lists: Sherman lists: SeQuiLa lists: SGD lists: ShinyGO lists: SISYPHUS lists: SVA lists: ASC lists: SIMULATE lists: SILVA lists: SNP HITLINK lists: SIBLINK lists: SKAT lists: SimRare lists: SnoopCGH lists: SMRT View lists: SASQUANT lists: SIMPED lists: Sniffles lists: SIBMED lists: SMI Services lists: SOAPnuke lists: SGN lists: SIDER lists: SMART lists: ShortFuse lists: SWEEP lists: SnpSift lists: SOAPfusion lists: SNPTEST lists: SwissTree lists: TopFIND lists: Solas lists: SoupX lists: STEPS lists: FASTSLINK lists: SpliceMap lists: StSNP lists: Supersplat lists: Sybil lists: TAPIR: target prediction for plant microRNAs lists: SWISS-2DPAGE lists: SISSRs lists: T-lex lists: SUMSTAT lists: TAGS lists: Spot lists: TDR Targets Database lists: TDT-PC lists: SpoTyping lists: SynTView lists: SynergyFinder lists: TRAL lists: SPIKE lists: Transporter Classification Database lists: TransmiR lists: TASSEL lists: SYFPEITHI: A Database for MHC Ligands and Peptide Motifs lists: FLUX CAPACITOR lists: TB PORTALS lists: TAndem Splice Site DataBase lists: VirusHunter lists: topGO lists: TMAJ lists: ApiDB ToxoDB lists: tradeSeq lists: TreeDyn lists: Trans-ABySS lists: IQ-TREE lists: Biological General Repository for Interaction Datasets (BioGRID) lists: Trowel lists: TomoMiner lists: UTRdb/UTRsite lists: TWOLOC lists: V-Phaser 2 lists: TropGENE DB lists: Trim Galore lists: TRACESPipe lists: Gene Index Project lists: Tool recommender system in Galaxy lists: WEIGHTED FDR lists: UTGB Toolkit lists: xia2 pipeline lists: USeq lists: TRiCoLOR lists: UniParc lists: VAAST lists: variancePartition lists: VirusSeq lists: Webproanalyst lists: XPN lists: WSsas - Web Service for the SAS tool lists: UNAFold lists: zUMIs lists: VaDiR lists: Yeast Search for Transcriptional Regulators And Consensus Tracking lists: Vector Alignment Search Tool lists: Zebrafish Information Network (ZFIN) lists: YASARA lists: Vmatch lists: VFDB - Virulence Factors of Bacterial Pathogens lists: Xenbase lists: Visualization and Analysis of Networks containing Experimental Data (VANTED) lists: VisSR lists: AutoDock lists: dbEST lists: DESeq2 lists: DNA DataBank of Japan (DDBJ) lists: FASTX-Toolkit lists: SUP lists: Trimmomatic lists: VIPERdb lists: ABySS lists: AdapterRemoval lists: Alien-hunter lists: ALTree lists: Integrative Genomics Viewer lists: RDKit: Open-Source Cheminformatics Software lists: Acacia lists: AMAP lists: Anfo lists: Aragorn lists: Arden lists: Ariba lists: ART lists: Augustus lists: Axe lists: Baitfisher lists: BALLView lists: BEAGLE lists: BEDOPS lists: eXpress lists: BOXSHADE 3.21 lists: Cassiopee lists: Cdbfasta lists: Circlator lists: Clearcut lists: Clonalframe lists: ClonalOrigin lists: Computational Morphometry Toolkit lists: Concavity lists: CRAC lists: cwltool lists: Daligner lists: Datamash lists: DNACLUST lists: DWGSIM lists: Eigensoft lists: EMBOSS lists: ESTScan lists: EULER-SR lists: FASTLINK lists: FigTree lists: fitGCP lists: Fsm-lite lists: Gamgi lists: GASiC lists: Ghemical lists: GIIRA lists: Grinder lists: Gwyddion lists: Hmmer lists: HTQC lists: IDBA-UD lists: ImageJ lists: Infernal lists: PyMOL lists: GenABEL lists: Biopython lists: QuorUM lists: Prodigal lists: QuteMol lists: PRESTO: Genetic Association Analysis Software lists: Probalign lists: Computational Structural Biology Toolbox lists: LEfSe lists: Happy lists: jModelTest lists: KMC lists: LAMARC lists: libRoadRunner lists: LoFreq lists: MetaPhlAn lists: MicrobiomeUtilities lists: MINIMAC lists: MIPE lists: mothur lists: Mugsy lists: GNU Octave lists: Oncofuse lists: PBSIM lists: PerlPrimer lists: PHAST lists: Picard lists: PLINK lists: ADEGENET lists: phytools lists: PSCBS lists: R/QTL lists: SAM lists: vegan lists: RepeatMasker lists: Scythe lists: SEER lists: Seq-Gen lists: SMRT-Analysis lists: Scalable Nucleotide Alignment Program lists: SPAdes lists: TraceTuner lists: Transterm lists: TreeView lists: Viewmol lists: Vascular Modeling Toolkit lists: Aegean lists: amide lists: Anndata lists: ANTS - Advanced Normalization ToolS lists: ARB project lists: ArtificialFastqGenerator lists: Arvados lists: Bandage lists: Berkeley Advanced Reconstruction Toolbox lists: BBmap lists: Eagle lists: Bio-Formats lists: BioImage Suite lists: BioJava Project lists: BioSig: An Imaging Bioinformatics System for Phenotypic Analysis lists: BRAKER lists: Bustools lists: Computerized Anatomical Reconstruction and Editing Toolkit lists: CellProfiler Image Analysis Software lists: ChIPSeq Peak Finder lists: ChromHMM lists: Cluster lists: Cytoscape lists: Dazzler lists: DCMTK: DICOM Toolkit lists: DeepNano lists: dinifti lists: DICOMscope lists: Dipy lists: Drop-seq tools lists: Electronic Cell Project lists: Ecopcr lists: Edtsurf lists: DOMAINATRIX lists: DOMALIGN lists: Embassy-domsearch lists: E-mem lists: e-PCR lists: Falcon lists: Fastaq lists: Fastqtl lists: Ffindex lists: FreeSurfer lists: FSA lists: FSL lists: Galaxy lists: GARLI lists: Garlic lists: IndelGenotyper lists: gdpc lists: Gemma lists: GenomeTools lists: Gentle lists: GERP lists: Gff2aplot lists: gffread lists: GraPhlAn lists: Gubbins lists: Harvest-tools lists: HiLive lists: Hinge lists: ImageMagick lists: ImageVis3D lists: Indelible lists: InVesalius 3 lists: IQ TREE lists: ITK-SNAP lists: JBrowse lists: JIST: Java Image Science Toolkit lists: Fastahack lists: Lipsia lists: LUMPY lists: Mash lists: Mesquite lists: MetaBAT lists: MOSAIK lists: MRtrix lists: Human Disease Ontology lists: NanoFilt lists: Object-Oriented Development Interface for NMR lists: OpenElectrophy lists: OpenMEEG lists: OpenWalnut lists: OptiType lists: PARASAIL lists: ParaView lists: PhyloPhlAn lists: Phyutility lists: Porechop lists: PSIPRED lists: PsychoPy lists: Pychopper lists: pydicom lists: PySurfer lists: MNE software lists: pbcore lists: pyxnat lists: QIIME2 lists: RAxML Next Generation lists: ShortRead lists: Phangorn lists: psych lists: VennDiagram lists: Recognition of Errors in Assemblies using Paired Reads lists: RELION lists: RStudio lists: Salmon lists: Scoary lists: University of Zurich SCRM - Cell-and Tissue Biobank lists: Short Read Sequence Typing for Bacterial Pathogens lists: Umap lists: VoxBo lists: WTDBG lists: XNAT - The Extensible Neuroimaging Archive Toolkit lists: ABACAS lists: AceDB lists: LINKAGE lists: Protein Information Resource lists: PredictNLS lists: tRNAscan-SE lists: RSEM lists: Aeskulap lists: alleleCount lists: assembly-stats lists: Atropos lists: Assemblytics lists: Augur lists: AxParafit lists: Aghermann lists: bambamc lists: AxPcoords lists: bamkit lists: BAli-Phy lists: Auspice lists: BBHash lists: BCALM 2 lists: Bibus lists: BioMAJ lists: BioCocoa lists: Biber lists: BioImageXD lists: caftools lists: BOLT-LMM lists: CamiTK lists: CLI for BioMAJ lists: CAMP lists: CAT and BAT lists: CHIME lists: CDK lists: ChromImpute lists: CiftiLib lists: conda-package-handling lists: CARD lists: CONTRAfold lists: CodonW lists: Change-O lists: C Thread Pool lists: Chemtool lists: covtobed lists: CTK lists: CTDopts lists: CTDConverter lists: Conquest DICOM lists: CTSim lists: Dicom3tools lists: Dendroscope3 lists: cyvcf2 lists: Deepbinner lists: EDFlib lists: EDFbrowser lists: dicompyler lists: EMMAX lists: DEXTRACTOR lists: DNApi lists: Epigrass lists: ELPH lists: ExaBayes lists: EMPeror lists: FreeImage lists: Fast5 Library lists: Entangle lists: FFP lists: GenomeTester4 lists: Filtlong lists: EMBOSS explorer lists: GfaPy lists: GATB lists: GCLib lists: EpiFire lists: HTSJDK lists: GDCM lists: GNUmed lists: GraphMap2 lists: foreign lists: Ginkgo CADx lists: GramAlign lists: IDeFIX lists: ImageTooth lists: Htscodecs lists: IGoR lists: iVar lists: InsPecT lists: Intake lists: IgDiscover lists: JAligner lists: ISMRMRD lists: JabRef lists: Lambda lists: Kaptive lists: KBibTeX lists: InSilicoSeq lists: kineticsTools lists: AcePerl lists: KmerResistance lists: Bio-EUtilities lists: Insight Toolkit lists: Kleborate lists: KMA lists: kempbasu lists: Bio-ASN1-EntrezGene lists: IVA lists: Bio-Coordinate lists: Bio-Graphics lists: AI-FANN lists: Bio-Chado-Schema lists: BioD lists: Bio-Tools-Run-Alignment-Clustalw lists: Bio-PrimerDesigner lists: Bioparser lists: Edlib lists: Bio-SamTools lists: libdisorder lists: libncl lists: Bio-Tools-Run-Alignment-TCoffee lists: Chado lists: Bio-Tools-Phylo-PAML lists: libGDF lists: JLODA lists: libdivsufsort lists: libminc lists: Bio-SCF lists: Sort-Key-Top lists: Java NeXML libraries and tools lists: libmaus2 lists: libqes lists: MIA lists: libics lists: FAST Analysis of Sequences Toolbox lists: Libchipcard lists: TaxonomyTree lists: Core Wrapper lists: Lighter lists: SSW Library lists: libqc++ lists: SeqLib lists: tabixpp lists: libStatGen lists: ThreadPool lists: Lucy lists: MafFilter lists: Metastudent lists: Libxdf lists: limereg lists: Mapsembler2 lists: MAXFLOW lists: metaBIT lists: MacSyFinder lists: VIGRA lists: MCL lists: MHAP lists: MindTheGap lists: Logol lists: medicalterms lists: mmtf-python lists: Miniasm lists: Tab2MAGE lists: MView lists: LTRsift lists: Molekel lists: mirtop lists: Maude lists: MicrobeGPS lists: mPSQed lists: mPTP lists: SMILE lists: Entrez Direct lists: NW-align lists: NanoSV lists: Mustang lists: Nanocall lists: Ngila lists: MRtrix3 lists: NORSp lists: Murasaki lists: Nextflow lists: NCBI accession download script lists: omegaMap lists: NJplot lists: NanoLyse lists: OpenCFU lists: NORSnet lists: OBITools lists: NeoBio lists: OptimiR lists: PartitionFinder lists: OpenSurgSim lists: NanoPlot lists: NextSV lists: OpenEMR lists: Orthanc lists: PAIPline lists: Odil lists: PHYLOViZ lists: PlasmidSeeker lists: PDB2PQR lists: OpenIGTLink lists: Parsnp lists: parallel-fastq-dump lists: ParsInsert lists: PiGx-RNAseq lists: PfTools lists: PlasmidID lists: Phyx lists: pipasic lists: pngquant lists: pbcopper lists: Patristic lists: PLIP lists: Placnet lists: PhySamp lists: pufferfish lists: PRINSEQ lists: PLAST lists: PCMA lists: picopore lists: POA lists: PROFisis lists: ProDA lists: PRANK lists: Cooler lists: pyepl lists: pssh2 lists: Plastimatch lists: pynast lists: psignifit lists: python-airr lists: Populations lists: pyFAI lists: python-biom-format lists: pyranges lists: purple lists: PyCogent lists: qtlreaper lists: qcumber lists: python-bx lists: pyomo lists: pycoqc lists: Proteinortho lists: DendroPy lists: qtltools lists: pyscanfcs lists: rambo-k lists: qcat lists: rasmol lists: rampler lists: raccoon lists: ragout lists: rapmap lists: quicktree lists: Raster3D lists: AnnotationHub lists: Rate4Site lists: altcdfenvs lists: annotate lists: biomformat lists: Biobase lists: affyio lists: bridgedbr lists: BiocGenerics lists: biovizBase lists: genefilter lists: CNEr lists: bsgenome lists: geneplotter lists: ctc lists: genomicalignments lists: go.db lists: genomeinfodb lists: hypergraph lists: gviz lists: groHMM lists: mergeomics lists: impute lists: makecdfenv lists: multiassayexperiment lists: qusage lists: mutationalpatterns lists: metagenomeseq lists: preprocesscore lists: pwmenrich lists: rbgl lists: htsfilter lists: nanostringqcpro lists: rgsepd lists: rcpi lists: pcaMethods lists: adephylo lists: rsamtools lists: savr lists: tfbstools lists: xvector lists: ade4 lists: biwt lists: beeswarm lists: cmprsk lists: alakazam lists: bio3d lists: Epi lists: BoolNet lists: DT lists: DoseFinding lists: itertools lists: fitdistrplus lists: fitbitscraper lists: dynamicTreeCut lists: epibasix lists: distory lists: forecast lists: incidence lists: hms lists: nmf lists: mediana lists: genetics lists: lexrankr lists: psychometric lists: optimalcutpoints lists: proc lists: pcapp lists: parmigene lists: rann lists: phylobase lists: psyphy lists: psychotree lists: rnexml lists: rook lists: rpact lists: tigger lists: robustrankaggreg lists: qqman lists: rwave lists: shazam lists: rsvd lists: rncl lists: rotl lists: rniftilib lists: sjplot lists: wavethresh lists: stringi lists: snowfall lists: waveslim lists: surveillance lists: tsne lists: webgestaltr lists: resfinder lists: readucks lists: recan lists: roadtrips lists: readseq lists: roguenarok lists: rtax lists: rgfa lists: ruby-bio lists: runcircos-gui lists: sailfish lists: samclip lists: saint lists: sambamba lists: seqmagick lists: sbmltoolbox lists: seq-seq-pan lists: seqsero lists: seqwish lists: shapeit4 lists: sepp lists: crb-blast lists: sigma-align lists: sibsim4 lists: signalalign lists: sibelia lists: shiny-server lists: sistr lists: skesa lists: sigviewer lists: snpomatic lists: spaced lists: sitplus lists: sofa-apps lists: sra-toolkit lists: strap-base lists: sparta lists: swarm lists: sourmash lists: surankco lists: streamlit lists: tab2mage lists: sumaclust lists: sweed lists: tacg lists: zAlign lists: tiddit lists: Workrave lists: sprai lists: VolPack lists: XMedCon lists: Yanosim lists: Yanagiba lists: libswiss-perl lists: yaha lists: VisIt lists: VelvetOptimiser lists: variation graph lists: vcfanno lists: VarMatch lists: VirulenceFinder lists: CCS lists: VADR lists: VARNA lists: VMD lists: FISH lists: trace2dbEST lists: TREE-PUZZLE lists: umis lists: Trinculo lists: toil lists: TRANSIT lists: toppred lists: Unicycler lists: TM-align lists: Tn-seq explorer lists: Tombo lists: TopHat-Recondition is related to: FreeContact is parent organization of: neurodebian |
Free, Freely available | nlx_151598 | SCR_006638 | Debian - The universal operating system, Debian GNU/Linux | 2026-08-03 09:33:11 | 50 | |||||||
|
Comparative Toxicogenomics Database (CTD) Resource Report Resource Website 1000+ mentions |
Comparative Toxicogenomics Database (CTD) (RRID:SCR_006530) | CTD | production service resource, data analysis service, service resource, database, analysis service resource, data or information resource | A public database that enhances understanding of the effects of environmental chemicals on human health. Integrated GO data and a GO browser add functionality to CTD by allowing users to understand biological functions, processes and cellular locations that are the targets of chemical exposures. CTD includes curated data describing cross-species chemical–gene/protein interactions, chemical–disease and gene–disease associations to illuminate molecular mechanisms underlying variable susceptibility and environmentally influenced diseases. These data will also provide insights into complex chemical–gene and protein interaction networks. | environment, chemical, disease, gene, pathway, protein, interaction, animal model, ontology, annotation, toxin, ontology or annotation browser, FASEB list |
is used by: DisGeNET is used by: NIF Data Federation is listed by: 3DVC is listed by: Gene Ontology Tools is related to: PharmGKB Ontology is related to: Gene Ontology is related to: BioRAT is related to: Integrated Gene-Disease Interaction is related to: OMICtools is related to: Integrated Manually Extracted Annotation has parent organization: Mount Desert Island Biological Laboratory has parent organization: North Carolina State University; North Carolina; USA is parent organization of: Interaction Ontology |
Pfizer ; American Chemistry Council ; NIEHS ES014065; NIEHS R01 ES019604; NCRR P20 RR016463; NIEHS U24 ES033155 |
PMID:16902965 PMID:16675512 PMID:14735110 PMID:12760826 |
Free, Freely available | OMICS_01578, nif-0000-02683, r3d100011530 | http://ctd.mdibl.org, https://doi.org/10.17616/R3KS7N | SCR_006530 | CTD - Comparative Toxicogenomics Database | 2026-08-03 09:33:06 | 1188 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that RRID has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on RRID then you can log in from here to get additional features in RRID such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into RRID you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
