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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Kismeth Resource Report Resource Website 50+ mentions |
Kismeth (RRID:SCR_005444) | Kismeth | analysis service resource, data analysis service, production service resource, service resource | A web-based tool for bisulfite sequencing analysis that was designed to be used with plants, since it considers potential cytosine methylation in any sequence context (CG, CHG, and CHH). It provides a tool for the design of bisulfite primers as well as several tools for the analysis of the bisulfite sequencing results. Kismeth is not limited to data from plants, as it can be used with data from any species. | plant, methylation, bisulfite sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Icahn School of Medicine at Mount Sinai; New York; USA |
PMID:18786255 | Free for academic use, Contact for commercial use | biotools:kismeth, OMICS_00602 | https://bio.tools/kismeth | SCR_005444 | 2026-09-19 12:56:51 | 55 | ||||||
|
TRANSFAC Resource Report Resource Website 100+ mentions |
TRANSFAC (RRID:SCR_005620) | TRANSFAC | data or information resource, database | Manually curated database of eukaryotic transcription factors, their genomic binding sites and DNA binding profiles. Used to predict potential transcription factor binding sites. | Curated, eucaryotic, transcription, factor, genomic, binding, site, sequence, regulated, gene, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: Gene Regulation Databases is related to: TRANSPATH is related to: Babelomics is related to: GeneTrail works with: rVista |
European Commission ; German Ministry of Education and Research |
PMID:12520026 | Free, Freely available | biotools:transfac, nif-0000-03576 | http://www.biobase-international.com/pages/index.php?id=transfac, http://gene-regulation.com/pub/databases.html, https://bio.tools/transfac | SCR_005620 | 2026-09-19 12:56:52 | 266 | |||||
|
UniCarb-DB Resource Report Resource Website 1+ mentions |
UniCarb-DB (RRID:SCR_014407) | data or information resource, database | An experimental glycomic MS database initially created to meet the in-house need to store structural and MS-glycomic data. Users can search by taxonomy and tissue, mass and composition, and MS/MS. | database, carbohydrate, glycomic ms, spectral library, structural ms, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Gothenburg; Gothenburg; Sweden has parent organization: UniCarbKB |
Nectar ; Australian National Data Service ; Swedish Foundation for International Cooperation in Research and Higher Education ; Swiss Institute of Bioinformatics ExPASy |
DOI:10.1093/bioinformatics/btr137 | Available to the research community | biotools:unicarb-db | https://bio.tools/unicarb-db | SCR_014407 | UniCarb-DB structural- MS spectral library database | 2026-09-19 12:57:33 | 8 | |||||
|
ApiDB ToxoDB Resource Report Resource Website 100+ mentions |
ApiDB ToxoDB (RRID:SCR_013453) | ApiDB ToxoDB | data or information resource, database | A genome and functional genomic database for the protozoan parasite Toxoplasma gondii. It incorporates the sequence and annotation of the T. gondii ME49 strain, as well as genome sequences for the GT1, VEG and RH (Chr Ia, Chr Ib) strains. Sequence information is integrated with various other genomic-scale data, including community annotation, ESTs, gene expression and proteomics data. Organisms * Toxoplasma gondii (ME49, RH, GT1, Veg strains) * Neospora caninum * environmental isolate sequences from numerous species Tools * BLAST: Identify Sequence Similarities * Sequence Retrieval: Retrieve Specific Sequences using IDs and coordinates * PubMed and Entrez: View the Latest Toxoplasma, Neospora Pubmed and Entrez Results * Genome Browser: View Sequences and Features in the genome browser * Ancillary Genome Browse: Access Additional info like Probeset data and Toxoplasma Array info | end-sequencing, bac clone, data mining tool, microarray, proteomic sequencing, toxoplasma gondii, bac clone, 8x random shotgun, genomic sequencing project, snp, qtl, sequencing, genomic, non-vertebrate, unicellular, eukaryote, genome, pathogen, toxoplasmosis, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: Eukaryotic Pathogen Database Resources |
NIAID contract HHSN266200400037C | PMID:18003657 PMID:12519989 |
r3d100012266, biotools:toxodb, nif-0000-03572 | https://bio.tools/toxodb | http://ToxoDB.org | SCR_013453 | Toxoplasma Genomics Resource, ToxoDB | 2026-09-19 12:57:31 | 153 | ||||
|
HUGE - Human Unidentified Gene-Encoded large proteins Resource Report Resource Website 10+ mentions |
HUGE - Human Unidentified Gene-Encoded large proteins (RRID:SCR_013482) | data or information resource, database | The HUGE protein database has been created to publicize the Human cDNA project at the Kazusa DNA Research Institute. This project will sequence and analyze long (>4 kb) human cDNAs and establish methods by using the sequence data how to predict the primary structure of proteins of various biological activities. Currently, it focuses on the analysis of cDNA clones encoding particularly large proteins (>50 kDa). The HUGE protein database contains various types of information derived from the predicted primary structure data of newly identified human proteins. The HUGE protein database are expected to cover various sets of large human proteins of hitherto unidentified functions. They are likely to be involved in cellular structure/motility (such as cytoskeleton, membrane skeleton, and motor proteins), gene expression and nucleic acid metabolism, cell signaling/communication (such as cellular adhesion, signal transduction, channels, and receptors), and so on. | cdna, human protein, bio.tools |
is listed by: bio.tools is listed by: Debian |
nif-0000-02990, biotools:huge | https://bio.tools/huge | SCR_013482 | HUGE | 2026-09-19 12:57:31 | 17 | ||||||||
|
KAVIAR Resource Report Resource Website 10+ mentions |
KAVIAR (RRID:SCR_013737) | data or information resource, database | A database containing a compilation of SNVs, indels, and complex variants observed in humans, designed to facilitate testing for the novelty and frequency of observed variants. | SNV, single nucleotide variant, database, indel, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Institute for Systems Biology; Washington; USA |
Inova Translational Medicine Institute | PMID:21965822 | Free, Public | biotools:kaviar | https://bio.tools/kaviar | SCR_013737 | queryable database of known variants, Known VARiants | 2026-09-19 12:57:32 | 18 | |||||
|
MobiDB Resource Report Resource Website 100+ mentions |
MobiDB (RRID:SCR_014542) | data or information resource, database | A database of protein disorder and mobility annotations. The database features three levels of annotation: manually curated data (which are extracted from the DisProt database), indirect data, and predicted data. Additional annotations are included from external sources, including UniProt, Pfam, PDB, and STRING. | database, protein disorder, mobility, annotation, intrinsic protein disorder, bio.tools, FASEB list |
uses: UniProt uses: STRING uses: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) uses: Pfam is listed by: bio.tools is listed by: Debian has parent organization: University of Padua; Padua; Italy |
Available to the research community | biotools:mobidb | https://bio.tools/mobidb | SCR_014542 | 2026-09-19 12:57:33 | 145 | ||||||||
|
Research-tested Intervention Programs (RTIPs) Resource Report Resource Website 10+ mentions |
Research-tested Intervention Programs (RTIPs) (RRID:SCR_016042) | RTIPs | data or information resource, database | Database of cancer control interventions and program materials. It is designed to provide program planners and public health practitioners easy and immediate access to research-tested materials. | cancer, control, intervention, prevention, diagnosis, planning, research, program, public, health, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian |
cancer | NCI | Freely available, Public | biotools:rtips | https://bio.tools/rtips | SCR_016042 | Research-tested Intervention Programs | 2026-09-19 12:57:35 | 25 | ||||
|
3D-footprint Resource Report Resource Website |
3D-footprint (RRID:SCR_015713) | data or information resource, database | Database of DNA-binding protein structures that is updated with Protein Data Bank complexes. It provides structure-based binding specificities and sequence logos, classification and clusters of protein-DNA interfaces, and downloads/stats. | dna binding protein structure, protein data bank, sequencing, protein-dna interface, bio.tools |
is listed by: Debian is listed by: bio.tools works with: footprintDB |
CSIC 200720I038 | PMID:19767616 | Freely available, Free for academic use, Tutorial available | biotools:3d-footprint | https://bio.tools/3d-footprint | SCR_015713 | 2026-09-19 12:57:35 | 0 | ||||||
|
ProteomicsDB Resource Report Resource Website 100+ mentions |
ProteomicsDB (RRID:SCR_015562) | data or information resource, database | Database for the identification of the human proteome and its use across the scientific community. Users can browse proteins and chromosomes and contribute to the data repository. | human proteome, human proteomics, proteomics database, human proteomics database, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools is related to: ProteomeTools has parent organization: Technical University of Munich; Bavaria; Germany |
PMID:24870543 | The research community can contribute to this resource | r3d100013408, biotools:proteomicsdb | https://bio.tools/proteomicsdb, https://doi.org/10.17616/R31NJMU8 | SCR_015562 | 2026-09-19 12:57:35 | 180 | |||||||
|
EGSEA Resource Report Resource Website 50+ mentions |
EGSEA (RRID:SCR_015036) | software resource, software toolkit, source code | Method developed for RNA-sequencing data. EGSEA combines results from twelve algorithms and calculates collective gene set scores to improve the biological relevance of the highest ranked gene sets. | gene set, rna sequencing, analysis method, r package, bio.tools |
is listed by: Debian is listed by: bio.tools is hosted by: Bioconductor |
Victorian State Government Operational Infrastructure Support ; Australian Government NHMRC IRIISS ; NHMRC GNT1050661; NHMRC GNT1045936; NHMRC GNT1057854; NHMRC GNT1104924 |
PMID:27694195 | Free, Available for download | biotools:egsea | https://bio.tools/egsea | SCR_015036 | Ensemble of Gene Set Enrichment Analyses (EGSEA), Ensemble of Gene Set Enrichment Analyses | 2026-09-19 12:57:34 | 64 | |||||
|
Datasets2Tools Resource Report Resource Website 1+ mentions |
Datasets2Tools (RRID:SCR_016174) | data or information resource, database | Database for the discovery and evaluation of biomedical digital objects. It includes a wide variety of enrichment analyses, gene interaction networks, interactive data visualizations, datasets, and computational tools. | biomedical, digital, bioinformatics, dataset, rna seq, computation, microarray, proteomic, bio.tools |
is listed by: bio.tools is listed by: Debian |
Public, Freely available | biotools:datasets2tools | https://bio.tools/datasets2tools | SCR_016174 | 2026-09-19 12:57:35 | 1 | ||||||||
|
TransmiR Resource Report Resource Website 100+ mentions |
TransmiR (RRID:SCR_017499) | data or information resource, database | Collection of transcription factor microRNA regulations. TransmiR v2.0 manually curated TF-miRNA regulations from publications during 2013-2017 and included ChIP-seq-derived TF-miRNA regulation data. | Transcription, factor, miRNA, regulation, manually, curated, TF-miRNA, ChIPseq, derived, TF-miRNA, data, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: Peking University; Beijing; China |
Restricted | biotools:transmir | https://bio.tools/transmir/ | SCR_017499 | TransmiR v2.0 | 2026-09-19 12:57:36 | 123 | |||||||
|
HmtVar Resource Report Resource Website 10+ mentions |
HmtVar (RRID:SCR_017288) | data or information resource, database, service resource | Manually curated database offering variability and pathogenicity information about mtDNA variants. Human mitochondrial variants data of healthy and diseased subjects.Data and text mining pipeline to annotate human mitochondrial variants with functional and clinical information. | manually, curated, data, variability, mitochondria, pathogenicity, mtDNA, variant, human, bio.tools |
uses: HmtDB - Human Mitochondrial DataBase uses: 1000 Genomes Project and AWS uses: MITOMAP - A human mitochondrial genome database uses: MutPred uses: SNPsandGO is listed by: Debian is listed by: bio.tools is affiliated with: University of Bologna; Bologna; Italy has parent organization: University of Bari; Bari; Italy |
DHOMOS Worldwide Cancer Research ; DISCO TRIP ; Italian Ministry of Health ; Rosa Maria Massari fellowship from the Italian Association for Cancer Research |
PMID:30371888 PMID:31821723 |
Free, Freely available | biotools:HmtVar | https://bio.tools/HmtVar | SCR_017288 | 2026-09-19 12:57:36 | 12 | ||||||
|
Blood Exposome Database Resource Report Resource Website 10+ mentions |
Blood Exposome Database (RRID:SCR_017610) | data or information resource, database | Collection of chemical compounds and associated information that were automatically extracted by text mining content of PubMed and PubChem databases. Unifies chemical lists from metabolomics, systems biology, environmental epidemiology, occupational expossure, toxiology and nutrition fields. | Chemical, compound, collection, extracted, text, mining, PubMed chemical compounds list, PubChem chemical compounds list, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of California at Davis; California; USA |
NIAID U54 AI138370; NIA U19 AG023122; NIEHS U2C ES030158 |
PMID:31557052 | Free, Available for download, Freely available | biotools:blood-exposome-db | https://github.com/barupal/exposome, https://bio.tools/blood-exposome-db | SCR_017610 | The Blood Exposome Database, exposome | 2026-09-19 12:57:37 | 11 | |||||
|
PEPPER Resource Report Resource Website 1+ mentions |
PEPPER (RRID:SCR_000431) | PEPPER | software application, software resource | A Cytoscape app designed to identify protein pathways / complexes as densely connected subnetworks from seed lists of proteins derived from pull-down assays (i.e AP-MS...). | plugin, protein-protein interaction, network, bio.tools |
is listed by: OMICtools is listed by: Cytoscape is listed by: bio.tools is listed by: Debian |
PMID:25138169 | Free, Available for download, Freely available | biotools:pepper, OMICS_05485 | https://bio.tools/pepper | SCR_000431 | Protein complex Expansion using Protein-Protein intERaction networks, Protein complex Expansion using Protein-Protein intERactions | 2026-09-19 12:57:41 | 1 | |||||
|
LOCUSMAP Resource Report Resource Website |
LOCUSMAP (RRID:SCR_000840) | LOCUSMAP | software application, software resource | Software package designed for rapid linkage analysis and map construction of loci with a variety of inheritance modes. (entry from Genetic Analysis Software) | gene, genetic, genomic, fortran 90/95, ms-windows, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154434, biotools:locusmap | https://bio.tools/locusmap | SCR_000840 | 2026-09-19 12:57:42 | 0 | ||||||||
|
circlize Resource Report Resource Website 1000+ mentions |
circlize (RRID:SCR_002141) | software application, software resource, standalone software | Software package that implements and enhances circular visualization in R. Due to natural born feature of R to draw statistical graphics, this package can provide more general and flexible way to visualize huge information in circular style. | circular visualization, draw statistical graphics, circular style graphics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: CRAN |
PMID:24930139 | Free, Available for download, Freely available | OMICS_04658, biotools:circlize | https://github.com/jokergoo/circlize, https://bio.tools/circlize | SCR_002141 | circlize: Circular Visualization in R | 2026-09-19 12:57:44 | 1289 | ||||||
|
GERMLINE Resource Report Resource Website 100+ mentions |
GERMLINE (RRID:SCR_001720) | GERMLINE | software application, software resource | Software application for discovering long shared segments of Identity by Descent (IBD) between pairs of individuals in a large population. It takes as input genotype or haplotype marker data for individuals (as well as an optional known pedigree) and generates a list of all pairwise segmental sharing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, c++, linux, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: Columbia University; New York; USA |
PMID:18971310 | Free, Available for download, Freely available | biotools:germline, OMICS_00202, nlx_154080 | https://bio.tools/germline | http://www1.cs.columbia.edu/~gusev/germline/ | SCR_001720 | 2026-09-19 12:57:44 | 451 | |||||
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BREAKDANCER Resource Report Resource Website 100+ mentions |
BREAKDANCER (RRID:SCR_001799) | BreakDancer | software application, software resource | A Perl/C++ software package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation. (entry from Genetic Analysis Software) | gene, genetic, genomic, perl, c++, next generation sequencing, structural variant, insertion, deletion, inversion, inter-chromosomal translocation, intra-chromosomal translocation, chromosomal translocation, indel, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
PMID:19668202 | Free, Available for download, Freely available | biotools:breakdancer, nlx_154253, OMICS_00307 | https://bio.tools/breakdancer | SCR_001799 | 2026-09-19 12:57:44 | 390 |
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