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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Magic Resource Report Resource Website 500+ mentions |
Magic (RRID:SCR_006406) | MAGIC | data or information resource, database, service resource | Web based interface for exploring and analyzing a comprehensive maize-specific cross-platform expression compendium. This compendium was constructed by collecting, homogenizing and formally annotating publicly available microarrays from Gene Expression Omnibus (GEO), and ArrayExpress. | gene expression, microarray, development stage, annotation, line, perturbation, gene, contrast, pathway, locus tag, bio.tools, FASEB list |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Gene Expression Omnibus is related to: ArrayExpress is related to: Plant Ontology is related to: Gene Ontology has parent organization: Ghent University; Ghent; Belgium |
PMID:24407224 | biotools:magic, OMICS_02206 | https://bio.tools/magic | SCR_006406 | MAGIC - MAize Gene expressIon Compendium, MAize Gene expressIon Compendium | 2026-02-15 09:19:16 | 706 | ||||||
|
Hyper Cell Line Database Resource Report Resource Website |
Hyper Cell Line Database (RRID:SCR_007730) | HyperCLDB | material resource, tissue bank, biomaterial supply resource | Hypertext on cell culture availability extracted from the Cell Line Data Base of the Interlab Project. HyperCLDB includes links to records of OMIM, the Online Mendelian Inheritance in Man Catalogue, and now also links to the PubMed, database of bibliographic biomedical references, which are drawn primarily from MEDLINE and PREMEDLINE. | cell, cell line, tumor, tissue, organ, blood, bodily fluid, ascitic fluid, brain, bone marrow, cancer, transforming agent, software, bio.tools |
is listed by: One Mind Biospecimen Bank Listing is listed by: 3DVC is listed by: Debian is listed by: bio.tools is related to: ATCC is related to: Cell Line Knowledge Base has parent organization: IST National Institute for Cancer Research; Genoa; Italy |
Cancer, Etc. | PMID:18927105 | nif-0000-03004, biotools:hypercldb | https://bio.tools/hypercldb | SCR_007730 | 2026-02-15 09:19:39 | 0 | ||||||
|
IRESite Resource Report Resource Website 10+ mentions |
IRESite (RRID:SCR_007753) | data or information resource, database | Database of experimentally verified IRES structures. Presents information about experimentally studied Internal Ribosome Entry Site segments. | bio.tools, experimentally verified IRES structures, Internal Ribosome Entry Site segments, IRES structures, IRES segments |
is listed by: bio.tools is listed by: Debian has parent organization: Charles University; Prague; Czech Republic |
nif-0000-03047, nif-0000-03046, SCR_007754, biotools:iresite | https://bio.tools/iresite | http://ifr31w3.toulouse.inserm.fr/IRESdatabase/ | SCR_007753 | IRESdb, , IRESdb - the Internal Ribosome Entry Site database, Internal Ribosome Entry Site | 2026-02-15 09:19:47 | 45 | |||||||
|
Single Nucleotide Polymorphism Spectral Decomposition (SNPSpD) Resource Report Resource Website 10+ mentions |
Single Nucleotide Polymorphism Spectral Decomposition (SNPSpD) (RRID:SCR_008621) | SNPSpD | service resource, analysis service resource, data analysis service, production service resource | SNPSpD is a method of correcting for non-independance of single nucleotide polymorphisms (SNPs) in linkage disequilibrium (LD) with each other, on the basis of the spectral decomposition (SpD) of matrices of LD between SNP''s. Additionally, output from SNPSpD includes eigenvalues, principal-component coefficients, and factor loadings after varimax rotation, enabling the selection of a subset of SNPs that optimize the information in a genomic region. | bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Queensland Institute of Medical Research |
National Health and MRC Australia 241916 | PMID:14997420 | biotools:snpspd, nif-0000-31985 | https://bio.tools/snpspd | http://genepi.qimr.edu.au/general/daleN/SNPSp | SCR_008621 | Single Nucleotide Polymorphism Spectral Decomposition | 2026-02-15 09:19:52 | 18 | ||||
|
Webproanalyst Resource Report Resource Website |
Webproanalyst (RRID:SCR_008348) | service resource, analysis service resource, data analysis service, production service resource | WebProAnalyst provides web-accessible analysis for scanning the quantitative structure-activity relationships in protein families. It searches for a sequence region, whose substitutions are correlated with variations in the activities of a homologous protein set, the so-called activity modulating sites. WebProAnalyst allows users to search for the key physicochemical characteristics of the sites that affect the changes in protein activities. It enables the building of multiple linear regression and neural networks models that relate these characteristics to protein activities. WebProAnalyst implements multiple linear regression analysis, back propagation neural networks and the Structure-Activity Correlation/Determination Coefficient (SACC/SADC). A back propagation neural network is implemented as a two-layered network, one layer as input, the other as output (Rumelhart et al, 1986). WebProAnalyst uses alignment of amino acid sequences and data on protein activity (pK, Km, ED50, among others). The input data are the numerical values for the physicochemical characteristics of a site in the multiple alignment given by a slide window. The output data are the predicted activity values. The current version of WebProAnalyst handles a single activity for a single protein. The SACC/SADC may be defined as an estimate of the strongest multiple correlation between the physicochemical characteristics of a site in a multiple alignment and protein activities. The SACC/SADC coefficient makes possible the calculation of the possible highest correlation achievable for the quantitative relationship between the physicochemical properties of sites and protein activities. The SACC/SADC is a convenient means for an arrangement of positions by their functional significance. WebProAnalyst outputs a list of multiple alignment positions, the respective correlation values, also regression analysis parameters for the relationships between the amino acid physicochemical characteristics at these positions and the protein activity values. | family, functional, activity, alignment, amino acid, homologous, modulating site, neural, physicochemical, propagation, protein, quantitative, region, relationship, scan, sequence, structure, substitution, variation, bio.tools |
is listed by: bio.tools is listed by: Debian |
nif-0000-25212, biotools:webproanalyst | https://bio.tools/webproanalyst | SCR_008348 | Webproanalyst | 2026-02-15 09:19:47 | 0 | ||||||||
|
SPIKE Resource Report Resource Website 100+ mentions |
SPIKE (RRID:SCR_010466) | SPIKE | data or information resource, database, service resource | Database of curated human signaling pathways with an associated interactive software tool for analysis and dynamic visualization of pathways. Individual pathway maps can be viewed and downloaded; the entire database may be browsed, or launched via a map viewer tool that allows dynamic visualization of the database and save networks in XGMML format that can be viewed in all generic XGMML viewers. Map Topics * Cell cycle progress and check points * DNA damage response * Programmed cell death related processes * Stress-activated transcription factors * Mitogen-activated protein kinase pathways * Immune response signaling * HEarSpike: hearing related pathways | visualization, analysis, cellular, signaling pathway, regulatory network, function, genomic, proteomic, cell cycle, dna damage, cell death, stress, transcription factor, mitogen, protein kinase, pathway, immune response, signaling, hearing, dna damage response, programmed cell death, development, ear, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is related to: ConsensusPathDB has parent organization: Tel Aviv University; Ramat Aviv; Israel |
Cancer | A-T Children's Project ; Wolfson Foundation ; European Union FP7 ; Israel Science Foundation |
PMID:21097778 PMID:18289391 |
biotools:spike, nlx_157705 | https://bio.tools/spike | SCR_010466 | Signaling Pathway Integrated Knowledge Engine | 2026-02-15 09:20:21 | 128 | ||||
|
NEBcutter Resource Report Resource Website 100+ mentions |
NEBcutter (RRID:SCR_010664) | service resource, analysis service resource, data analysis service, production service resource | This tool will take a DNA sequence and find the large, non-overlapping open reading frames using the E.coli genetic code and the sites for all Type II and commercially available Type III restriction enzymes that cut the sequence just once. By default, only enzymes available from NEB are used, but other sets may be chosen. Just enter your sequence and submit. Further options will appear with the output. The maximum size of the input file is 1 MByte, and the maximum sequence length is 300 KBases. NEBcutter produces a variety of outputs including restriction enzyme maps, theoretical digests and links into the restriction enzyme database, REBASE (http://rebase.neb.com/rebase/rebase.html). Importantly, its table of recognition sites is updated daily from REBASE and it marks all sites that are potentially affected by DNA methylation (Dam, Dcm, etc.). Many options exist to choose the enzymes used for digestion, including all known specificities, subsets of those that are commercially available or sets of enzymes that produce compatible termini. | bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: New England Biolabs |
PMID:12824395 | biotools:nebcutter, nlx_71778 | https://bio.tools/nebcutter | SCR_010664 | 2026-02-15 09:20:01 | 142 | ||||||||
|
ComiR Resource Report Resource Website 10+ mentions |
ComiR (RRID:SCR_013023) | ComiR | service resource, analysis service resource, data analysis service, production service resource | Data analysis service that predicts whether a given mRNA is targeted by a set of miRNAs. ComiR uses miRNA expression to improve and combine multiple miRNA targets for each of the four prediction algorithms: miRanda, PITA, TargetScan and mirSVR. The composite scores of the four algorithms are then combined using a support vector machine trained on Drosophila Ago1 IP data. | mirna, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Pittsburgh; Pennsylvania; USA |
NLM ; Fondazione RiMED |
PMID:23703208 PMID:23284279 |
Acknowledgement requested | OMICS_00395, biotools:comir | https://bio.tools/comir | SCR_013023 | Combinatorial miRNA targeting, ComiR: Combinatorial miRNA target prediction tool, ComiR - Combinatorial miRNA target prediction tool | 2026-02-15 09:20:41 | 26 | ||||
|
omiRas Resource Report Resource Website 10+ mentions |
omiRas (RRID:SCR_010833) | omiRas | service resource, analysis service resource, data analysis service, production service resource | A web server for the annotation, comparison and visualization of interaction networks of non-coding RNAs derived from small RNA-Sequencing experiments of two different conditions. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23946503 | biotools:omiras, OMICS_00383 | https://bio.tools/omiras | SCR_010833 | 2026-02-15 09:20:25 | 14 | |||||||
|
MutationTaster Resource Report Resource Website 1000+ mentions |
MutationTaster (RRID:SCR_010777) | MutationTaster | service resource, analysis service resource, data analysis service, production service resource | Evaluates disease-causing potential of sequence alterations. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
PMID:20676075 | Acknowledgement requested | biotools:mutation_taster, OMICS_00153 | https://bio.tools/mutation_taster | SCR_010777 | 2026-02-15 09:20:03 | 4180 | ||||||
|
GenoREAD Resource Report Resource Website |
GenoREAD (RRID:SCR_012007) | GenoREAD | service resource, analysis service resource, data analysis service, production service resource | A sequence verification pipeline where users can submit trace files to verify if a clone''s physical sequence matches its reference sequence. | clone, verification, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Virginia Bioinformatics Institute |
PMID:23042248 | Acknowledgement requested | OMICS_01823, biotools:genoread | https://bio.tools/genoread | SCR_012007 | GenoREAD - Sequencing Verification Pipeline | 2026-02-15 09:20:28 | 0 | |||||
|
PLAN2L Resource Report Resource Website |
PLAN2L (RRID:SCR_013346) | PLAN2L | data or information resource, database, service resource | A web-based online search system that integrates text mining and information extraction techniques to access systematically information useful for analyzing genetic, cellular and molecular aspects of the plant model organism Arabidopsis thaliana. The system facilitates a more efficient retrieval of information relevant to heterogeneous biological topics, from implications in biological relationships at the level of protein interactions and gene regulation, to sub-cellular locations of gene products and associations to cellular and developmental processes, i.e. cell cycle, flowering, root, leaf and seed development. Beyond single entities, also predefined pairs of entities can be provided as queries for which literature-derived relations together with textual evidences are returned. | text mining, bio-entity relation extraction, literature, information extraction, cell cycle, regulation, protein interaction, cellular location, flowering, leave, root, seed, gene, normalization, interaction, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Spanish National Cancer Research Center |
PMID:19520768 | OMICS_01192, biotools:plan2l | https://bio.tools/plan2l | SCR_013346 | PLAN2L: Plant Annotation to Literature, Plant annotation to literature | 2026-02-15 09:20:40 | 0 | ||||||
|
DSAP Resource Report Resource Website 1+ mentions |
DSAP (RRID:SCR_013352) | DSAP | service resource, analysis service resource, data analysis service, production service resource | A web server designed to provide a total solution to analyze small RNAs sequencing data generated by SOLEXA., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:20478825 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:dsap, OMICS_00357 | https://bio.tools/dsap | SCR_013352 | 2026-02-15 09:20:43 | 8 | ||||||
|
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 |
Rosa Maria Massari fellowship from the Italian Association for Cancer Research ; DHOMOS Worldwide Cancer Research ; DISCO TRIP ; Italian Ministry of Health |
PMID:30371888 PMID:31821723 |
Free, Freely available | biotools:HmtVar | https://bio.tools/HmtVar | SCR_017288 | 2026-02-15 09:21:18 | 10 | ||||||
|
EGSEA Resource Report Resource Website 50+ mentions |
EGSEA (RRID:SCR_015036) | source code, software toolkit, software resource | 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 | 2026-02-15 09:21:05 | 62 | |||||
|
HOMOZYGOSITYMAPPER Resource Report Resource Website 100+ mentions |
HOMOZYGOSITYMAPPER (RRID:SCR_001714) | HomozygosityMapper | service resource, analysis service resource, data analysis service, production service resource | A web-based approach of homozygosity mapping that can handle tens of thousands markers. User can upload their own SNP genotype files to the database. Intuitive graphic interface is provided to view the homozygous stretches, with the ability of zooming into single chromosomes or user-defined chromosome regions. The underlying genotypes in all samples are displayed. The software is also integrated with our candidate gene search engine, GeneDistiller, so that users can interactively determine the most promising gene. (entry from Genetic Analysis Software) | gene, genetic, genomic, perl, genotype, homozygosity score, homozygosity, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: Charite - Universitatsmedizin Berlin; Berlin; Germany |
PMID:19465395 | Free, Freely Available | nlx_154069, biotools:homozygositymapper, OMICS_00123 | https://bio.tools/homozygositymapper | SCR_001714 | 2026-02-15 09:18:09 | 121 | ||||||
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Identifiers.org Resource Report Resource Website 50+ mentions |
Identifiers.org (RRID:SCR_003735) | Identifiers.org | identifier resolution, service resource, production service resource | A system providing resolvable persistent Uniform Resource Identifiers (URIs) used to identify data for the scientific community, with a current focus on the Life Sciences domain. The provision of resolvable identifiers (URLs) fits well with the Semantic Web vision, and the Linked Data initiative. It provides direct access to the identified data using one chosen physical location (or resource). If more than one physical locations providing the data are recorded in the Registry, then you can access them via the top banner or by using a profile. | identifier, life sciences, bio.tools |
uses: MIRIAM Resources is listed by: bio.tools is listed by: Debian has parent organization: European Bioinformatics Institute |
Free | nlx_157931, biotools:identifiers.org | https://bio.tools/identifiers.org | SCR_003735 | 2026-02-15 09:18:34 | 50 | |||||||
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INMEX Resource Report Resource Website 10+ mentions |
INMEX (RRID:SCR_004173) | INMEX | service resource, analysis service resource, data analysis service, production service resource | A web-based tool to support meta-analysis of multiple gene-expression data sets, as well as to enable integration of data sets from gene expression and metabolomics experiments. INMEX contains three functional modules. The data preparation module supports flexible data processing, annotation and visualization of individual data sets. The statistical analysis module allows researchers to combine multiple data sets based on P-values, effect sizes, rank orders and other features. The significant genes can be examined in functional analysis module for enriched Gene Ontology terms or Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, or expression profile visualization. INMEX has built-in support for common gene/metabolite identifiers (IDs), as well as 45 popular microarray platforms for human, mouse and rat. Complex operations are performed through a user-friendly web interface in a step-by-step manner. | gene expression, meta-analysis, metabolomics, pathway, gene, metabolite, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology is related to: KEGG is related to: Human Metabolome Database has parent organization: University of British Columbia; British Columbia; Canada |
Killam Trust ; Canadian Institutes of Health Research |
PMID:23766290 | Acknowledgement requested | biotools:inmex, OMICS_01546 | https://bio.tools/inmex | SCR_004173 | INtegrative Meta-analysis of EXpression data, INMEX - INtegrative Meta-analysis of EXpression data | 2026-02-15 09:18:38 | 19 | ||||
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VIPERdb Resource Report Resource Website 50+ mentions |
VIPERdb (RRID:SCR_002853) | data or information resource, database | Database for icosahedral virus capsid structures. The emphasis of the resource is on providing data from structural and computational analyses on these systems, as well as high quality renderings for visual exploration. In addition, all virus capsids are placed in a single icosahedral orientation convention, facilitating comparison between different structures. The web site includes powerful search utilities , links to other relevant databases, background information on virus capsid structure, and useful database interface tools. It is an information source for the analysis of high resolution virus structures. VIPERdb is a one-stop site dedicated to helping users around the world examine the many icosahedral virus structures contained within the Protein Data Bank (PDB) by providing them with an easy to use database containing current data and a variety of analytical tools. Sponsors: VIPERdb is funded by the NIH., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | exploration, analysis, capsid, computational, convention, database, icosahedral, structural, structure, system, virus, visual, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian has parent organization: Scripps Research Institute |
PMID:33313778 PMID:30265627 |
Free, Freely available | nif-0000-25311, r3d100012362, nif-0000-03630, biotools:viperdb, SCR_007970 | https://bio.tools/viperdb https://doi.org/10.17616/R3HT0Q |
SCR_002853 | Virus Particle ExploreR | 2026-02-15 09:18:23 | 59 | ||||||
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Proteome Analyst Specialized Subcellular Localization Server Resource Report Resource Website 1+ mentions |
Proteome Analyst Specialized Subcellular Localization Server (RRID:SCR_003143) | PA-SUB | service resource, analysis service resource, data analysis service, production service resource | Web server specialized to predict the subcellular localization of proteins using established machine learning techniques. | subcellular localization, protein, machine learning, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Alberta; Alberta; Canada |
PMID:14990451 | Free, Available for download, Freely available | biotools:pa-sub, OMICS_01631 | https://psort.org/#:~:text=Proteome%20Analyst's%20Subcellular%20Localization%20Server proteins%20to%20many%20localization%20sites. |
SCR_003143 | 2026-02-15 09:18:29 | 1 |
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