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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | |||||
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PARASAIL Resource Report Resource Website 1+ mentions |
PARASAIL (RRID:SCR_021805) | alignment software, data processing software, image analysis software, software application, software resource | Software tool as multiple sequence alignement for global, local and semi global alignments. | multiple sequence alignement, global alignments, local alignments, semi global alignments, | is listed by: Debian | Pacific Northwest National Laboratory | DOI:10.1186/s12859-016-0930-z | Free, Available for download, Freely available | https://sources.debian.org/src/libparasail-dev/ | SCR_021805 | Pairwise Sequence Alignment Library | 2026-09-19 12:54:58 | 4 | ||||||
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ToppCluster Resource Report Resource Website 100+ mentions |
ToppCluster (RRID:SCR_001503) | ToppCluster | analysis service resource, data analysis service, production service resource, resource, service resource | A tool for performing multi-cluster gene functional enrichment analyses on large scale data (microarray experiments with many time-points, cell-types, tissue-types, etc.). It facilitates co-analysis of multiple gene lists and yields as output a rich functional map showing the shared and list-specific functional features. The output can be visualized in tabular, heatmap or network formats using built-in options as well as third-party software. It uses the hypergeometric test to obtain functional enrichment achieved via the gene list enrichment analysis option available in ToppGene. | term enrichment, gene, analysis, gene enrichment analysis, connectivity, heatmap, ortholog, microarray, function, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: GenitoUrinary Development Molecular Anatomy Project is related to: ToppGene Suite |
NIDDK 1U01DK70219; NIDDK P30DK078392; NCRR U54 RR025216; NIDCR U01DE020049 |
PMID:20484371 | Free | OMICS_02225, nlx_152801, biotools:toppcluster | https://bio.tools/toppcluster | SCR_001503 | ToppCluster: A multiple gene list feature analyzer for the dissection of biological systems | 2026-09-19 12:55:04 | 152 | ||||
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StatAlign Resource Report Resource Website 1+ mentions |
StatAlign (RRID:SCR_001892) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software package for Bayesian analysis of protein, DNA and RNA sequences. It utilizes multiple alignments, phylogenetic trees and evolutionary parameters to quantify uncertainty in these analyses. It is written in Java. | software package, bayesian, protein, dna, rna, sequencing, java, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) |
PMID:23335014 | Free, Available for download, Freely available | biotools:StatAlign, OMICS_03743 | https://bio.tools/StatAlign | SCR_001892 | StatAlign 2.0 | 2026-09-19 12:55:04 | 1 | ||||||
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FACTA+. Resource Report Resource Website 1+ mentions |
FACTA+. (RRID:SCR_001767) | FACTA+ | data access protocol, service resource, software resource, web service | Text mining tool to discover associations between biomedical concepts from MEDLINE articles. Use the service from your browser or via a Web Service. The whole MEDLINE corpus containing more than 20 million articles is indexed with an efficient text search engine, and it allows you to navigate such associations and their textual evidence in a highly interactive manner - the system accepts arbitrary query terms and displays relevant concepts immediately. A broad range of important biomedical concepts are covered by the combination of a machine learning-based term recognizer and large-scale dictionaries for genes, proteins, diseases, and chemical compounds. There is also a FACTA+ visualization service that can be found here: http://www.nactem.ac.uk/facta-visualizer/ | text mining, gene, protein, disease, symptom, drug, enzyme, compound, biomedical, association, machine learning, chemical, text-mining software, bio.tools |
is listed by: OMICtools is listed by: FORCE11 is listed by: bio.tools is listed by: Debian is related to: MEDLINE has parent organization: National Centre for Text Mining |
JISC | PMID:18772154 | Free, Freely available | biotools:facta_plus, nif-0000-10272, OMICS_01181 | http://refine1-nactem.mc.man.ac.uk/facta/, https://bio.tools/facta_plus | SCR_001767 | Finding Associated Concepts with Text Analysis | 2026-09-19 12:55:04 | 2 | ||||
|
FusionCatcher Resource Report Resource Website 1+ mentions |
FusionCatcher (RRID:SCR_000060) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software that searches for novel/known fusion genes, translocations, and chimeras in RNA-seq data (paired-end reads from Illumina NGS platforms like Solexa and HiSeq) from diseased samples. | fusion gene, known fusion gene, translocation, chimera, rna-seq data, hiseq, solexa, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1101/011650 | Free, Available for download, Freely available | biotools:fusioncatcher, OMICS_01348 | https://github.com/ndaniel/fusioncatcher/blob/master/doc/manual.md, https://bio.tools/fusioncatcher | http://code.google.com/p/fusioncatcher/ | SCR_000060 | 2026-09-19 12:55:03 | 9 | ||||||
|
Dissect Resource Report Resource Website |
Dissect (RRID:SCR_000058) | Dissect | alignment software, data processing software, image analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software transcriptome-to-genome alignment tool, which can identify and characterize transcriptomic events such as duplications, inversions, rearrangements and fusions. | Structural events containing transcripts, transcriptome-to-genome alignment, identify and characterize transcriptomic events, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: Simon Fraser University; British Columbia; Canada |
PMID:22689759 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01346, biotools:dissect | https://bio.tools/dissect | SCR_000058 | Dissect: DIScovery of Structural Events Containing Transcripts, DIScovery of Structural Events Containing Transcripts | 2026-09-19 12:55:03 | 0 | |||||
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cpnDB: A Chaperonin Database Resource Report Resource Website 1+ mentions |
cpnDB: A Chaperonin Database (RRID:SCR_002263) | cpnDB | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | A curated collection of chaperonin sequence data collected from public databases or generated by a network of collaborators exploiting the cpn60 target in clinical, phylogenetic and microbial ecology studies. The database contains all available sequences for both group I and group II chaperonins. Users can search the database by Chaperonin type, group (I or II), BLAST, or other options, and can also enter and analyze FASTA sequences. | chaperonin sequence, microbial ecology, phylogenetics, chaperonin, plastid, mitochondria, cytoplasm, sequence, blast, fasta, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Canadian Biotechnology Strategy ; National Research Council Genomics and Health Initiative |
PMID:15289485 | Free, Freely available | biotools:cpndb, OMICS_01511, nif-0000-02694 | https://bio.tools/cpndb | http://www.cpndb.ca/cpnDB/home.php | SCR_002263 | 2026-09-19 12:55:05 | 4 | ||||
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Predictions for Entire Proteomes Resource Report Resource Website 500+ mentions |
Predictions for Entire Proteomes (RRID:SCR_002803) | data analysis software, data processing software, sequence analysis software, software application, software resource, web application | Web application for sequence analysis and the prediction of protein structure and function. The user interface intakes protein sequences or alignments and returned multiple sequence alignments, motifs, and nuclear localization signals., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 15,2026. | sequence analysis database, protein structure prediction, protein structure, protein function, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: Columbia University; New York; USA |
BMBF | PMID:24799431 DOI:10.1093/nar/gkh377 |
THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-00136, OMICS_07135, biotools:predictprotein | https://bio.tools/predictprotein, https://sources.debian.org/src/predictprotein/ | http://cubic.bioc.columbia.edu/pep/ | SCR_002803 | PredictProtein | 2026-09-19 12:55:05 | 643 | ||||
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RegulonDB Resource Report Resource Website 100+ mentions |
RegulonDB (RRID:SCR_003499) | RegulonDB | data or information resource, database | Database on transcriptional regulation in Escherichia coli K-12 containing knowledge manually curated from original scientific publications, complemented with high throughput datasets and comprehensive computational predictions. Graphic and text-integrated environment with friendly navigation where regulatory information is always at hand. They provide integrated views to understand as well as organized knowledge in computable form. Users may submit data to make it publicly available. | transcription, gene regulation, operon, bacteria, evolutionary conservation, regulatory phrase, transcriptional regulation, transcriptional regulatory network, bio.tools, FASEB list |
is listed by: OMICtools is listed by: 3DVC is listed by: bio.tools is listed by: Debian has parent organization: National Autonomous University of Mexico; Mexico City; Mexico |
NIGMS GM071962; NIGMS GM077678; Consejo Nacional de Ciencia y Tecnologia 103686; Consejo Nacional de Ciencia y Tecnologia 179997; Programa de Apoyo a Proyectos de Investigacion e Innovacion Tecnologica IN210810; Programa de Apoyo a Proyectos de Investigacion e Innovacion Tecnologica IN209312 |
PMID:23203884 | OMICS_01868, nif-0000-03399, biotools:regulondb | https://bio.tools/regulondb | SCR_003499 | 2026-09-19 12:55:06 | 153 | ||||||
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ProteomeXchange Resource Report Resource Website 5000+ mentions |
ProteomeXchange (RRID:SCR_004055) | catalog, consortium, data or information resource, data repository, database, organization portal, portal, service resource, storage service resource | A data repository for proteomic data sets. The ProteomeExchange consortium, as a whole, aims to provide a coordinated submission of MS proteomics data to the main existing proteomics repositories, as well as to encourage optimal data dissemination. ProteomeXchange provides access to a number of public databases, and users can access and submit data sets to the consortium's PRIDE database and PASSEL/PeptideAtlas. | consortium, database, proteomics, MS proteomics, protein, mass spectrometry, bio.tools, FASEB list |
uses: Proteomics Identifications (PRIDE) uses: PeptideAtlas is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: bio.tools is listed by: Debian is affiliated with: Omics Discovery Index is related to: Proteomics Identifications (PRIDE) is related to: PeptideAtlas is related to: SIB Swiss Institute of Bioinformatics is related to: Mass spectrometry Interactive Virtual Environment (MassIVE) is related to: European Bioinformatics Institute is related to: ProteomeTools is related to: Integrated Proteome Resources has parent organization: European Bioinformatics Institute |
European Union 260558 | Public, The community can contribute to this resource | r3d100012122, nlx_158620, biotools:proteomexchange | http://proteomecentral.proteomexchange.org, https://bio.tools/proteomexchange, https://doi.org/10.17616/R32D29 | SCR_004055 | , ProteomeXchange, Proteome Exchange | 2026-09-19 12:55:07 | 6107 | ||||||
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ngLOC Resource Report Resource Website 10+ mentions |
ngLOC (RRID:SCR_003150) | ngLOC | analysis service resource, data analysis service, production service resource, service resource, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023.An n-gram-based Bayesian classifier that predicts subcellular localization of proteins both in prokaryotes and eukaryotes. The downloadable version of this software with source code is freely available for academic use under the GNU General Public License. | subcellular localization, protein, eukaryote, prokaryote, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:22780965 PMID:17472741 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01629, biotools:ngloc | https://bio.tools/ngloc | SCR_003150 | ngLOC - A Bayesian method for predicting protein subcellular localization | 2026-09-19 12:55:06 | 22 | |||||
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ImaGene Resource Report Resource Website 100+ mentions |
ImaGene (RRID:SCR_002178) | data analysis software, data processing software, software application, software resource | Software tool as convolutional neural network to quantify natural selection from genomic data.Supervised machine learning algorithm to predict natural selection and estimate selection coefficients from population genomic data. Can be used to estimate any parameter of interest from evolutionary population genetics model., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | microarray analysis, machine vision, convolutional neural network, quantify natural selection, genomic data, population genomic data, evolutionary population, genetics model, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Imperial College London ; Politecnico di Milano |
PMID:31757205 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:ImaGene, OMICS_00841 | https://github.com/mfumagalli/ImaGene, https://bio.tools/ImaGene | http://www.biodiscovery.com/software/imagene/ | SCR_002178 | 2026-09-19 12:55:04 | 405 | |||||
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QualitySNPng Resource Report Resource Website 1+ mentions |
QualitySNPng (RRID:SCR_002479) | data processing software, data visualization software, software application, software resource, standalone software | Software for the detection and visualization of single nucleotide polymorphisms (SNPs) from next generation sequencing data that uses a haplotype-based strategy. | single nucleotide polymorphism, haplotype strategy, next generation sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:23632165 | Free, Available for download, Freely available | biotools:qualitysnpng, OMICS_00070 | https://bio.tools/qualitysnpng | SCR_002479 | 2026-09-19 12:55:05 | 7 | |||||||
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PBSIM Resource Report Resource Website 10+ mentions |
PBSIM (RRID:SCR_002512) | simulation software, software application, software resource | Software that simulates PacBio reads by using either a model-based or sampling-based simulation. | pacbio simulation, model-based simulation, sampling-based simulation |
is listed by: OMICtools is listed by: Debian |
PMID:23129296 DOI:10.1093/bioinformatics/bts649 |
Free, Available for download, Freely available | OMICS_00253 | https://sources.debian.org/src/pbsim/ | SCR_002512 | PacBio reads simulator | 2026-09-19 12:55:05 | 11 | ||||||
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VIRsiRNAdb Resource Report Resource Website 1+ mentions |
VIRsiRNAdb (RRID:SCR_006108) | VIRsiRNAdb | analysis service resource, data analysis service, data or information resource, data repository, database, production service resource, service resource, storage service resource | VIRsiRNAdb is a curated database of experimentally validated viral siRNA / shRNA targeting diverse genes of 42 important human viruses including influenza, SARS and Hepatitis viruses. Submissions are welcome. Currently, the database provides detailed experimental information of 1358 siRNA/shRNA which includes siRNA sequence, virus subtype, target gene, GenBank accession, design algorithm, cell type, test object, test method and efficacy (mostly quantitative efficacies). Further, wherever available, information regarding alternative efficacies of above 300 siRNAs derived from different assays has also been incorporated. The database has facilities like search, advance search (using Boolean operators AND, OR) browsing (with data sorting option), internal linking and external linking to other databases (Pubmed, Genbank, ICTV). Additionally useful siRNA analysis tools are also provided e.g. siTarAlign for aligning the siRNA sequence with reference viral genomes or user defined sequences. virsiRNAdb would prove useful for RNAi researchers especially in siRNA based antiviral therapeutics development. | virus, sirna, shrna, gene, influenza, sars, hepatitis, sirna sequence, virus subtype, target gene, genbank accession, design algorithm, cell type, efficacy, target genome region, target object, experimental assay, off-target, sirna matching, reference viral sequence, influenza virus, hepatitis b virus, hpv, sars corona virus, viral genome, reference genome, align, sirna sequence, fasta, blast, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Institute of Microbial Technology; Chandigarh; India |
Influenza, SARS, Hepatitis, Infectious disease | Council of Scientific and Industrial Research; New Delhi; India | PMID:22139916 | Open unspecified license / Freely available | nlx_151610, biotools:virsirnadb | https://bio.tools/virsirnadb | SCR_006108 | VIRsiRNAdb - Database of Viral siRNA / shRNA, Viral siRNA Database, Viral siRNA Database (VIRsiRNAdb) | 2026-09-19 12:55:08 | 4 | |||
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qrqc Resource Report Resource Website 1+ mentions |
qrqc (RRID:SCR_006867) | qrqc | data analysis software, data processing software, sequence analysis software, software application, software resource | Software R package to quickly scan reads and gather statistics on base and quality frequencies, read length, k-mers by position, and frequent sequences. Produces graphical output of statistics for use in quality control pipelines, and an optional HTML quality report. S4 SequenceSummary objects allow specific tests and functionality to be written around the data collected. | Quickly scan reads, read length, k-mers, position, frequent sequences, quality control pipeline, HTML quality report, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:qrqc, OMICS_01071 | https://github.com/vsbuffalo/qrqc, https://bio.tools/qrqc | SCR_006867 | quick read quality control, Quick Read Quality Control | 2026-09-19 12:55:09 | 2 | ||||||
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SoyBase Resource Report Resource Website 500+ mentions |
SoyBase (RRID:SCR_005096) | SoyBase | analysis service resource, controlled vocabulary, data analysis service, data or information resource, data repository, database, ontology, production service resource, service resource, storage service resource | Professionally curated repository for genetics, genomics and related data resources for soybean that contains the most current genetic, physical and genomic sequence maps integrated with qualitative and quantitative traits. SoyBase includes annotated Williams 82 genomic sequence and associated data mining tools. The genetic and sequence views of the soybean chromosomes and the extensive data on traits and phenotypes are extensively interlinked. This allows entry to the database using almost any kind of available information, such as genetic map symbols, soybean gene names or phenotypic traits. The repository maintains controlled vocabularies for soybean growth, development, and traits that are linked to more general plant ontologies. Contributions to SoyBase or the Breeder''s Toolbox are welcome. | soybean, gene, genetic map, genome, data set, trait, phenotype, molecular biology, sequence, chromosome, quantitative trait locus, php, genetics, genomics, legume, bio.tools, FASEB list |
is listed by: 3DVC is listed by: re3data.org is listed by: Debian is listed by: bio.tools has parent organization: Iowa State University; Iowa; USA is parent organization of: Soybean Ontologies is parent organization of: Soy Ontology |
USDA Agricultural Research Service | PMID:20008513 | The community can contribute to this resource | nif-0000-03483, r3d100010846, biotools:soybase | https://bio.tools/soybase, https://doi.org/10.17616/R3S032 | SCR_005096 | SoyBase and the Soybean Breeder''s Toolbox, SoyBase and the Soybean Breeder''s Toolbox: Integrating Genetics and Molecular Biology for Soybean Researchers | 2026-09-19 12:55:07 | 830 | ||||
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Generic GO Term Mapper Resource Report Resource Website 10+ mentions |
Generic GO Term Mapper (RRID:SCR_005806) | GOTermMapper, GO Term Mapper | analysis service resource, data analysis service, data processing software, production service resource, service resource, software application, software resource | The Generic GO Term Mapper finds the GO terms shared among a list of genes from your organism of choice within a slim ontology, allowing them to be binned into broader categories. The user may optionally provide a custom gene association file or slim ontology, or a custom list of slim terms. The implementation of this Generic GO Term Mapper uses map2slim.pl script written by Chris Mungall at Berkeley Drosophila Genome Project, and some of the modules included in the GO-TermFinder distribution written by Gavin Sherlock and Shuai Weng at Stanford University, made publicly available through the GMOD project. GO Term Mapper serves a different function than the GO Term Finder. GO Term Mapper simply bins the submitted gene list to a static set of ancestor GO terms. In contrast, GO Term Finder finds the GO terms significantly enriched in a submitted list of genes. Platform: Online tool, Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible | gene ontology, gene, gene association, slim ontology, slimmer-type tool, term enrichment, gene annotation, genomics, ontology, process, function, component, bio.tools |
is listed by: Gene Ontology Tools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: Generic Model Organism Database Project has parent organization: Princeton University; New Jersey; USA |
Free for academic use | nlx_149294, biotools:go_term_mapper | https://bio.tools/go_term_mapper | SCR_005806 | Generic Gene Ontology Term Mapper, Generic Gene Ontology (GO) Term Mapper | 2026-09-19 12:55:08 | 45 | ||||||
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SOURCE Resource Report Resource Website 50+ mentions |
SOURCE (RRID:SCR_005799) | SOURCE | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | SOURCE compiles information from several publicly accessible databases, including UniGene, dbEST, UniProt Knowledgebase, GeneMap99, RHdb, GeneCards and LocusLink. GO terms associated with LocusLink entries appear in SOURCE. The mission of SOURCE is to provide a unique scientific resource that pools publicly available data commonly sought after for any clone, GenBank accession number, or gene. SOURCE is specifically designed to facilitate the analysis of large sets of data that biologists can now produce using genome-scale experimental approaches Platform: Online tool | genomic, functional annotation, ontology, gene expression, gene, genome, statistical analysis, bio.tools, FASEB list |
is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: SMD |
NIGMS ; NCI CA85129-04; NIGMS GM07365 |
PMID:12519986 | Restricted | biotools:source, nlx_149287 | https://login.stanford.edu/idp/profile/SAML2/Redirect/SSO?execution=e1s1, https://bio.tools/source | SCR_005799 | 2026-09-19 12:55:08 | 69 |
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