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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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DMRforPairs Resource Report Resource Website 1+ mentions |
DMRforPairs (RRID:SCR_005702) | software resource | Software for identifying differentially methylated regions between unique samples using array based methylation profiles. It allows researchers to compare n greater than or equal to 2 unique samples with regard to their methylation profile. The (pairwise) comparison of n unique single samples distinguishesit from other existing pipelines as these often compare groups of samples in either single CpG locus or region based analysis. DMRforPairs defines regions of interest as genomic ranges with sufficient probes located in close proximity to each other. Probes in one region are optionally annotated to the same functional class(es). Differential methylation is evaluated by comparing the methylation values within each region between individual samples and (if the difference is sufficiently large), testing this difference formally for statistical significance. | standalone software, mac os x, unix/linux, windows, r, annotation, dna methylation, differential methylation, microarray, report writing, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:24884391 | GNU General Public License, v2 or greater | biotools:dmrforpairs, OMICS_04059 | https://bio.tools/dmrforpairs | SCR_005702 | DMR2+, DMRforPairs: identifying Differentially Methylated Regions between unique samples using array based methylation profiles | 2026-09-12 12:56:30 | 4 | ||||||
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University of Lorraine; Lorraine; France Resource Report Resource Website 1+ mentions |
University of Lorraine; Lorraine; France (RRID:SCR_005705) | UL | university | French public university. | is parent organization of: Suggested Ontology for Pharmacogenomics | Wikidata:Q4173330, Crossref funder ID:100008990, nlx_158101, ISNI:0000 0001 2194 6418, grid.29172.3f | https://ror.org/04vfs2w97 | SCR_005705 | Universit� de Lorraine, University of Lorraine, Universite de Lorraine | 2026-09-12 12:56:30 | 1 | ||||||||
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MolGen Resource Report Resource Website 10+ mentions |
MolGen (RRID:SCR_005700) | MolGen | data or information resource, portal, topical portal | The research of the group concentrates on the molecular biology of Gram-positive bacteria, with Bacillus subtilis and Lactococcus lactis as the main model organisms. A number of important (human) pathogens are also investigated: Bacillus cereus, Streptococcus pneumoniae and Enterococcus faecalis. The nature of the research is both fundamental and application-oriented. Transcript- and protein profiling by high-throughput technologies such as DNA microarrays and proteomics tools are being used. The very large data sets generated are analyzed by employing existing and novel bioinformatics tools. Major lines of research are in the field of functional genomics of these organisms, using systems- and synthetic biology approaches. | molecular biology, gram-positive bacteria, pathogen, transcript, protein, profile, high-throughput, dna microarray, proteomics, dna, microarray, functional genomics, bioinformatics, genetics, gene |
has parent organization: University of Groningen; Groningen; Netherlands is parent organization of: FIVA - Functional Information Viewer and Analyzer |
nlx_149166 | http://molgen.biol.rug.nl/molgen/index.php | SCR_005700 | Molecular Genetics | 2026-09-12 12:56:30 | 28 | |||||||
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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 | data or information resource, department portal, organization portal, portal, software application, software resource, text-mining software | 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 | 2026-09-12 12:56:30 | 10 | |||||||
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Principe Felipe Research Centre; Valencia; Spain Resource Report Resource Website 1+ mentions |
Principe Felipe Research Centre; Valencia; Spain (RRID:SCR_005691) | CIPF | institution | The Pr��ncipe Felipe Research Centre (CIPF), which was inaugurated by their Royal Highnesses the Prince and Princess of Asturias on 17th March 2005, is a centre dedicated to biomedical research, with the aim of taking on new challenges in the field of basic research and encouraging scientific works of excellence. The construction of the Centre was carried out thanks to the Regional Development Funds from the European Union, and from the Regional Government (Generalitat Valenciana) through its Ministry of Health. The current financing of the CIPF comes mainly from the investment made by the Generalitat Valenciana through the Ministry of Health, as well as the Regenerative Medicine Programme, the fruit of an agreement between the Institute of Health Carlos III and the Ministry of Health for basic and translation research in this field. The CIPF takes the research tradition from the then Valencian Cytological Research Institute and the Valencian Biomedical Research Foundation, with the aim of consolidating and expanding this research. Therefore the activity in the CIPF can be divided into three main strategic work areas: The Regenerative Medicine area focuses its research on cellular therapy and interdisciplinary research in human embryonic and adult stem cells, with the aim of regenerating damaged organs to improve human health. The Chemical and Quantative Biology area aims to understand, through the application of (bio) chemical, genetic, and bioinformatic methods, to understand the molecular mechanisms that control the biological processes and alterations that lead to pathological conditions. The Biomedicine area focuses on understanding the molecular bases of human pathologies that require new diagnostic and clinical procedures for their identification and treatment, pathologies such as cancer, neurological pathologies and rare illnesses. |
is parent organization of: QualiMap is parent organization of: VARIANT is parent organization of: CIPF Bioinformatics and Genomics Department is parent organization of: Blast2GO is parent organization of: Gene Expression Profile Analysis Suite |
nlx_149142, grid.418274.c, ISNI: 0000 0004 0399 600X | https://ror.org/05xr2yq54 | SCR_005691 | Centro de Investigaci��n Pr��ncipe Felipe, Centro de Investigacion Principe Felipe, Principe Felipe Research Center, Pr��ncipe Felipe Research Centre | 2026-09-12 12:56:30 | 2 | ||||||||
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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 | data or information resource, department portal, institution, organization portal, 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 | 2026-09-12 12:56:30 | 5 | ||||||||
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VAGUE Resource Report Resource Website 1+ mentions |
VAGUE (RRID:SCR_005607) | VAGUE | software resource | An open-source de novo genome assembly software tool, which is run from the Unix command line, providing a multi-platform graphical front-end for the Velvet de novo assembler. VAGUE is implemented in JRuby and targets the Java Virtual Machine. | command line, assembler |
is listed by: OMICtools has parent organization: Monash University; Melbourne; Australia |
PMID:23162059 | GNU General Public License, v2, Acknowledgement requested | OMICS_00897 | SCR_005607 | Velvet Assembler Graphical Front End | 2026-09-12 12:56:28 | 5 | ||||||
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SeqGSEA Resource Report Resource Website 10+ mentions |
SeqGSEA (RRID:SCR_005724) | SeqGSEA | data analysis software, data processing software, software application, software resource | 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 | 2026-09-12 12:56:30 | 36 | |||||||
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Bismark Resource Report Resource Website 1000+ mentions |
Bismark (RRID:SCR_005604) | Bismark | software resource | Software tool to map bisulfite converted sequence reads and determine cytosine methylation states. Flexible aligner and methylation caller for Bisulfite-Seq applications. Used to map bisulfite treated sequencing reads to genome of interest and perform methylation calls in single step. | Map bisulfite treated sequence reads, determine cytosine methylation states, genome, sequence reads, perform methylation calls, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Babraham Institute |
PMID:21493656 DOI:10.1093/bioinformatics/btr167 |
Free, Available for download, Freely available | biotools:bismark, OMICS_00575 | https://github.com/FelixKrueger/Bismark, https://bio.tools/bismark | https://sources.debian.org/src/bismark/ | SCR_005604 | 2026-09-12 12:56:28 | 1200 | |||||
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Onto-Translate Resource Report Resource Website 1+ mentions |
Onto-Translate (RRID:SCR_005725) | Onto-Translate | analysis service resource, data analysis service, data or information resource, database, production service resource, 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 | 2026-09-12 12:56:30 | 3 | |||||||
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jMHC Resource Report Resource Website 10+ mentions |
jMHC (RRID:SCR_005605) | jMHC | software resource | Software for analyzing and visualization of the results of deep amplicon sequencing. | matlab |
is listed by: OMICtools has parent organization: Google Code |
PMID:21676201 | GNU General Public License, v3, Acknowledgement requested | OMICS_00300 | SCR_005605 | jmhc - software for analyzing and visualization of the results of deep amplicon sequencing | 2026-09-12 12:56:28 | 10 | ||||||
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ToppGene Suite Resource Report Resource Website 1000+ mentions |
ToppGene Suite (RRID:SCR_005726) | analysis service resource, data analysis service, data or information resource, database, portal, production service resource, resource, 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 | 2026-09-12 12:56:30 | 1131 | |||||
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TAIR Keyword Browser Resource Report Resource Website 10+ mentions |
TAIR Keyword Browser (RRID:SCR_005687) | TAIR Keyword Browser | analysis service resource, data analysis service, data or information resource, database, production service resource, 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 | 2026-09-12 12:56:29 | 37 | ||||||
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TMA-Combiner Resource Report Resource Website 1+ mentions |
TMA-Combiner (RRID:SCR_005600) | TMA-Combiner | software resource | A Simple Software Tool to Permit Analysis of Replicate Cores on Tissue Microarrays., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | tissue microarray |
is listed by: OMICtools is related to: Stanford TMA Software has parent organization: Stanford University; Stanford; California |
PMID:16258508 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00822 | SCR_005600 | 2026-09-12 12:56:28 | 1 | |||||||
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TMAJ Resource Report Resource Website 10+ mentions |
TMAJ (RRID:SCR_005601) | TMAJ | software resource | Open-source software to support information and images related to tissue micro-arrays. It contains support for multiple organ systems, multiple users, image analysis, and is designed to be compliant with HIPPA regulations. Patients, specimens, blocks, slides, cores, images, and scores can all be stored and viewed. Features include advanced security, custom dynamic fields, and an image analysis program. | tissue microarray, java, java swing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Johns Hopkins University; Maryland; USA has parent organization: SourceForge |
GNU General Public License, v3 | biotools:tmaj, OMICS_00823 | https://bio.tools/tmaj | SCR_005601 | TMAJ Software Project | 2026-09-12 12:56:28 | 10 | ||||||
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GOProfiler Resource Report Resource Website 1+ mentions |
GOProfiler (RRID:SCR_005683) | GOProfiler | service resource | Service that provides a summary of GO annotations available for each species. The user provides a taxon id and GOProfiler displays the number of GO associations and the number of annotated proteins for that species. The results are listed by evidence code and a separate list of unannotated proteins is also provided. | ontology or annotation browser, annotation, protein, gene ontology |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology has parent organization: AgBase |
PMID:16961921 | Free for academic use | OMICS_02269, nlx_149127 | SCR_005683 | 2026-09-12 12:56:29 | 2 | |||||||
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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 | analysis service resource, data analysis service, data or information resource, database, production service resource, 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 | 2026-09-12 12:56:29 | 2 | |||||
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GoFish Resource Report Resource Website 1+ mentions |
GoFish (RRID:SCR_005682) | GoFish | analysis service resource, data analysis service, production service resource, service resource, software resource, source code | Software program, available as a Java applet online or to download, allows the user to select a subset of Gene Ontology (GO) attributes, and ranks genes according to the probability of having all those attributes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, ontology or annotation browser, java, windows, mac os x, linux, unix, bio.tools |
is listed by: Gene Ontology Tools is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: University of Toronto; Ontario; Canada has parent organization: Harvard Medical School; Massachusetts; USA |
Aventis Pharmaceuticals ; Howard Hughes Medical Institute ; NHGRI |
PMID:12691998 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:gofish, nlx_149126, OMICS_02272 | http://llama.mshri.on.ca/Software.html, https://bio.tools/gofish | SCR_005682 | 2026-09-12 12:56:29 | 1 | |||||
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Hepatitis C Virus Database (HCVdb) Resource Report Resource Website 1+ mentions |
Hepatitis C Virus Database (HCVdb) (RRID:SCR_005718) | HCVdb, | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | The Hepatitis C Virus Database (HCVdb) is a cooperative project of several groups with the mission of providing to the scientific community studying the hepatitis C virus a comprehensive battery of informational and analytical tools. The Viral Bioinformatics Resource Center (VBRC), the Immune Epitope Database and Analysis Resource (IEDB), the Broad Institute Microbial Sequencing Center (MSC), and the Los Alamos HCV Sequence Database (HCV-LANL) are combining forces to acquire and annotate data on Hepatitis C virus, and to develop and utilize new tools to facilitate the study of this group of organisms. | hepatitis c, hepatitis c virus, genome, gene, virus, ortholog comparison, ortholog | has parent organization: VBRC | Hepatitis C virus | NIAID contract HHSN266200400036C | nlx_149175 | SCR_005718 | Hepatitis C Viral Database | 2026-09-12 12:56:30 | 4 | ||||||
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National Hellenic Research Foundation Resource Report Resource Website 1+ mentions |
National Hellenic Research Foundation (RRID:SCR_005719) | NHRF | institution | The National Hellenic Research Foundation (NHRF) is a multidisciplinary Research Centre established by Royal Decree on 9th October 1958. Its purpose is the organisation, finance and support of high-level research projects in the humanities and the natural sciences. The Humanities Institute cover a wide spectrum of study and research fields in Greek history and culture, contributing substantially and critically to the knowledge and promotion of Greek identity. The Natural Sciences Institutes perform basic and applied research in leading edge areas of science such as health, pharmaceuticals, environment, biotechnology and new materials. They develop innovative methods for solving complex problems facing Greek industry and they provide specialised services and know-how both to the public and private sector. The NHRF is governed by the Board of Directors and the Central Administration under the Director/Chairman of the Board. | humanities, natural sciences | is parent organization of: StRAnGER | ISNI: 0000 0001 2232 6894, grid.22459.38, Wikidata: Q1248816, nlx_149177 | https://ror.org/033m02g29 | SCR_005719 | National Hellenic Research Foundation | 2026-09-12 12:56:30 | 4 |
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