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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
ODAM Resource Report Resource Website 1+ mentions |
ODAM (RRID:SCR_018774) | data management software, data access protocol, software application, software repository, software resource, web service | Software experimental data table management system to make research data accessible and available for reuse with minimal effort on part of data provider. Allows any scientist or data researcher to be able to explore dataset and then extract some or all of data according to their needs. Designed to manage experimental data tables in quick and easy way for users. | Experimental data tables, research data management, OpenAPI, FAIR Data principles, assessment, EDTMS, data management, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | BioTools:ODAM, biotools:ODAM | https://bio.tools/ODAM, https://bio.tools/ODAM, https://bio.tools/ODAM, https://bio.tools/ODAM | SCR_018774 | Open Data for Access and Mining | 2026-08-05 10:47:05 | 3 | |||||||
|
ObjTables Resource Report Resource Website |
ObjTables (RRID:SCR_018652) | data processing software, data management software, software application, software toolkit, software resource | Software toolkit for creating reusable datasets that are both human and machine readable, combining spreadsheets with schemas including classes, their attributes, type of each attribute, and possible relationships between instances of classes.Consists of format for describing schemas for spreadsheets, numerous data types for science, syntax for indicating class and attribute represented by each table and column in workbook, and software for using schemas to rigorously validate, merge, split, compare, and revision datasets. Used for supplementary materials of journal article, as well as for emerging domains which need to quickly build new formats for new types of data and associated software with minimal effort. | Creating reusable dataset, combining spreadsheet with schema, spreadsheet, table, supplementary material, schema, object relational map, validation, bio.tools |
uses: BpForms uses: BcForms is listed by: bio.tools is listed by: Debian is related to: BpForms |
NIBIB P41 EB023912; NSF 1649014; NIGMS R35 GM119771 |
Free, Freely available | biotools:objtables | https://bio.tools/objtables | SCR_018652 | 2026-08-05 10:47:03 | 0 | |||||||
|
Preseq Resource Report Resource Website 10+ mentions |
Preseq (RRID:SCR_018664) | data processing software, software application, data analysis software, software toolkit, software resource | Software package for predicting library complexity and genome coverage in high throughput sequencing. Aimed at predicting yield of distinct reads from genomic library from initial sequencing experiment. Predicting molecular complexity of sequencing libraries. | Genome, high throughput sequencing, predicting library complexity, distinct yield prediction, genomic library, initial sequencing experiment, molecular complexity prediction, sequencing libraryb, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Stanford University; Stanford; California |
PMID:23435259 | Free, Freely available | biotools:preseq | https://github.com/smithlabcode/preseq, https://bio.tools/preseq | SCR_018664 | 2026-08-05 10:47:05 | 19 | |||||||
|
minet Resource Report Resource Website |
minet (RRID:SCR_018661) | data processing software, software application, data analysis software, software toolkit, software resource, network analysis software | Open source software R package for inferring large transcriptional networks using mutual information. Implements algorithms for inferring networks such as gene networks from microarray data. | Inferring transcriptional network, mutual information, gene network, microarray data, gene, statistical dependencies model, gene to gene interaciton, statistical quantification, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Bioconductor has parent organization: Free University of Brussels; Brussels; Belgium |
Communaute Francaise de Belgique | PMID:18959772 | Free, Available for download, Freely available | biotools:minet | http://minet.meyerp.com/, https://bio.tools/minet | SCR_018661 | Mutual Information NETworks | 2026-08-05 10:47:03 | 0 | |||||
|
MyGene.info Resource Report Resource Website 10+ mentions |
MyGene.info (RRID:SCR_018660) | data access protocol, service resource, software resource, web service | Web service for querying or retrieving gene annotation data. | Querying gene, gene, annotation, gene annotation, annotation data, gene annotation data, retrieving gene annotation data, bio.tools |
is listed by: Debian is listed by: bio.tools |
NHGRI U01 HG008473; NIGMS GM083924; NIGMS U54 GM114833; NHGRI U01 HG006476; NCI K22 CA188163; NCATS UL1 TR001114; Scripps Translational Science Institute |
DOI:10.1186/s13059-016-0953-9 | Free, Freely available | biotools:mygene.info, BioTools:mygene.info | https://bio.tools/mygene.info, https://bio.tools/mygene.info, https://bio.tools/mygene.info | SCR_018660 | 2026-08-05 10:47:05 | 20 | ||||||
|
AlgPred Resource Report Resource Website 50+ mentions |
AlgPred (RRID:SCR_018780) | data access protocol, service resource, software resource, web service | Web tool for prediction of allergens based on similarity of known epitope with any region of protein. Used for prediction of allergenic proteins and mapping of IgE epitopes. | Allergen prediction, allergenic protein, allergenic protein prediction, IgE epitopes mapping, epitope, protein region, prediction, bio.tools |
is listed by: Debian is listed by: bio.tools |
Council of Scientific and Industrial Research | PMID:16844994 | Free, Freely available | biotools:algpred | https://webs.iiitd.edu.in/raghava/algpred/submission.html, https://bio.tools/algpred | SCR_018780 | 2026-08-05 10:47:06 | 68 | ||||||
|
NanoGalaxy Resource Report Resource Website 1+ mentions |
NanoGalaxy (RRID:SCR_018912) | data processing software, data access protocol, software application, data visualization software, data analysis software, software toolkit, software resource, web service | Webserver to process, analyse and visualize Oxford Nanopore Technologies (ONT) data and similar long-reads technologies. Collection of best practice and popular ONT-oriented tools are integrated in this custom Galaxy instance. | European Galaxy Project, Oxford Nanopore Technologies, Oxford Nanopore Technologies data, data analysis, long reads technology, ONT oriented tools collection, custom Galaxy instance, , Galaxy, Nanopore, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Galaxy is related to: University of Freiburg; Baden-Wurttemberg; Germany |
Free, Freely available | biotools:nanogalaxy | https://galaxyproject.org/use/nanogalaxy/, https://bio.tools/nanogalaxy | SCR_018912 | 2026-08-05 10:47:06 | 9 | ||||||||
|
BadMedicine Resource Report Resource Website 1+ mentions |
BadMedicine (RRID:SCR_018879) | software development tool, software library, code testing framework, software application, software toolkit, software resource | Software library and command line tool for generating realistic looking synthetic Electronic Health Records data for testing purposes. | Electronic Health Record, electronic health record data generation, health data, testing health data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Freely available | biotools:badmedicine | https://bio.tools/badmedicine | SCR_018879 | 2026-08-05 10:47:06 | 1 | ||||||||
|
ScanITD Resource Report Resource Website 1+ mentions |
ScanITD (RRID:SCR_018886) | data processing software, software application, sequence analysis software, data analysis software, software resource | Open source software Python tool for detecting internal tandem duplication with variant allele frequency estimation. | Internal tandem duplication, FLT3, acute myeloid leukemia, TCGA, chimeric alignment, variant allele frequency, variant allele, frequency estimation, , bio.tools |
is listed by: Debian is listed by: bio.tools |
Acute Myeloid Leukemia | DOI:10.5524/100775 | Free, Available for download, Freely available | biotools:ScanItD | https://bio.tools/ScanITD, http://gigadb.org/dataset/100775 | SCR_018886 | Scan Internal Tandem Duplications | 2026-08-05 10:47:06 | 1 | |||||
|
TRiCoLOR Resource Report Resource Website 1+ mentions |
TRiCoLOR (RRID:SCR_018801) | data processing software, software application, sequence analysis software, data analysis software, software resource | Command line application for tandem repeats profiling from error prone long read sequencing data. Works on data from Oxford Nanopore Technologies and Pacific Biosciences sequencers. Used on whole genome alignments. | Tandem repeat, long read sequencing data, whole genome alignment, data analysis, sequence analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:tricolor | https://bio.tools/tricolor | SCR_018801 | 2026-08-05 10:47:05 | 2 | ||||||||
|
STAMP Resource Report Resource Website 500+ mentions |
STAMP (RRID:SCR_018887) | data processing software, software application, data visualization software, data analysis software, software toolkit, software resource | Open source software package for analyzing taxonomic or metabolic profiles that promotes best practices in choosing appropriate statistical techniques and reporting results. Graphical software package that provides statistical hypothesis tests and exploratory plots for analyzing taxonomic and functional profiles. Supports tests for comparing pairs of samples or samples organized into two or more treatment groups. | Statistical analysis, taxonomic profile, functional profile, metabolic profile, statistical hypothesis test, plot, sample, sample group, sample pair comparison, bio.tools |
is listed by: Debian is listed by: bio.tools |
Genome Atlantic ; Natural Sciences and Engineering Research Council of Canada ; Australian Research Council ; Canada Foundation for Innovation ; Canada Research Chairs program ; Dalhousie Faculty of Computer Science ; Dalhousie Centre for Comparative Genomics and Evolutionary Bioinformatics ; Tula Foundation Killam Trust |
PMID:25061070 | Free, Freely available | biotools:stamp-metagenomic | https://github.com/dparks1134/STAMP, https://github.com/dparks1134/STAMP/releases, https://bio.tools/stamp-metagenomic | SCR_018887 | STAMP v2.1.3, statistical analysis of taxonomic and functional profiles | 2026-08-05 10:47:07 | 504 | |||||
|
GOnet Resource Report Resource Website 1+ mentions |
GOnet (RRID:SCR_018977) | data access protocol, service resource, software resource, web service | Web tool for interactive Gene Ontology analysis of any biological data sources resulting in gene or protein lists. | Gene Ontology, interactive analysis, data, gene, protein, gene list, protein list, analysis, bio.tools |
is listed by: Debian is listed by: bio.tools works with: Gene Ontology |
NIH Common Fund ; NIGMS ; NHGRI R24 HG010032; NIAID U19 AI118610; NIAID U19 AI118626 |
PMID:30526489 | biotools:GOnet | https://github.com/mikpom/gonet, https://bio.tools/GOnet | SCR_018977 | 2026-08-05 10:47:07 | 3 | |||||||
|
EnteroBase Resource Report Resource Website 100+ mentions |
EnteroBase (RRID:SCR_019019) | data or information resource, data access protocol, software resource, database, web service | Integrated software environment that supports identification of global population structures within several bacterial genera that include pathogens. Web service for analyzing and visualizing genomic variation within bacteria. Genome database to enable to identify, analyse, quantify and visualise genomic variation within bacterial genera including Salmonella, Escherichia/Shigella, Clostridioides,Vibrio,Yersinia,Helicobacter,Moraxella. | Bacteria, pathogen, genome, Illumina short read, genotype, core genome multilocus, sequence typing, cgMLST, cgMLST sequence, bacterial strain mapping, visualizing genomic variation, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: University of Warwick; Coventry; United Kingdom |
Biotechnology and Biological Sciences Research Council ; Wellcome Trust |
Restricted | biotools:Enterobase | https://bio.tools/EnteroBase | SCR_019019 | 2026-08-05 10:47:08 | 233 | |||||||
|
D-GENIES Resource Report Resource Website 10+ mentions |
D-GENIES (RRID:SCR_018967) | data processing software, web application, image analysis software, software application, alignment software, standalone software, software resource | Open source software package developed in Python and JavaScript. Standalone and web application tool performing large genome alignments and generating interactive dot plots. Designed to compare two genomes. Used to sort query sequences along reference, zoom in plot and download several image, alignment or sequence files. Allows to display dot plots from other aligners by uploading their PAF or MAF alignment file. | bio.tools |
uses: Minimap2 is listed by: Debian is listed by: bio.tools |
PMID:29888139 | Free, Available for download, Freely available | biotools:d-genies | https://github.com/genotoul-bioinfo/dgenies, https://bio.tools/d-genies | SCR_018967 | Dot plot large GENomes in an Interactive, Efficient and Simple way | 2026-08-05 10:47:08 | 46 | ||||||
|
BiG-SLiCE Resource Report Resource Website 1+ mentions |
BiG-SLiCE (RRID:SCR_019130) | software resource, data processing software, software application, data analysis software | Software tool to perform large scale clustering analysis of Biosynthetic Gene Cluster data. | Biosynthetic Gene, gene clusters, super linear clustering, clustering data analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
Netherlands eScience Center Accelerating Scientific Discoveries Grant ; Graduate School for Experimental Plant Sciences Netherlands |
DOI:10.1101/2020.08.17.240838 | Free, Available for download, Freely available | biotools:big_slice | https://bio.tools/big_slice | SCR_019130 | Biosynthetic Gene clusters - Super Linear Clustering Engine | 2026-08-05 10:47:09 | 5 | |||||
|
Parliament2 Resource Report Resource Website 1+ mentions |
Parliament2 (RRID:SCR_019187) | data processing software, software application, data analysis software, software toolkit, software resource | Software tool to identify structural variants in given sample relative to reference genome. Runs combination of tools to generate structural variant calls on whole genome sequencing data. | structural variants identification, reference genome, structural variant calls generation, whole genome sequencing data, sequencing data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:parliament2 | https://bio.tools/parliament2 | SCR_019187 | 2026-08-05 10:47:10 | 5 | ||||||||
|
long-read-tools Resource Report Resource Website 10+ mentions |
long-read-tools (RRID:SCR_019116) | data or information resource, software repository, software resource, database | Interactive database of software tools for analysis of long read sequencing data.Catalogue of long-read sequencing data analysis tools. Catalogue of downstream analysis tools of real and synthetic long-read technologies. | Software tools collection, long read sequencing data, long read sequencing, data analysis, data analysis tools, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:32033565 | Free, Freely available | biotools:long-read-tools | https://github.com/shaniAmare/long_read_tools, https://bio.tools/long-read-tools | SCR_019116 | Long-Read-Tools, long-read-tools.org | 2026-08-05 10:47:10 | 11 | ||||||
|
runBioSimulations Resource Report Resource Website 1+ mentions |
runBioSimulations (RRID:SCR_019110) | software resource, web application | Web tool for executing broad range of modeling studies and visualizing their results. Provides web interface for reusing any model. Models, simulations, and visualizations are available under licenses specified for each resource. | Executing modeling studies, visualization, model reusing, simulation, bio.tools |
uses: BioSimulators is listed by: bio.tools is listed by: Debian |
Center for Reproducible Biomodeling Modeling ; National Institute of Bioimaging and Bioengineering ; National Institute of General Medical Sciences ; NSF ; NIH |
Free, Freely available | biotools:runbiosimulations | https://bio.tools/runbiosimulations | SCR_019110 | 2026-08-05 10:47:10 | 3 | |||||||
|
BioSimulators Resource Report Resource Website 1+ mentions |
BioSimulators (RRID:SCR_019111) | software resource, software repository, web application | Web tool as collection of containerized biosimulation tools that provide consistent interfaces and guide to choosing simulator. Helps to find simulation tools that have capabilities, including supported modeling frameworks, simulation algorithms, and modeling formats, needed for specific modeling projects. | Containerized biosimulation tools, consistent interfaces, choosing simulator guide, supported modeling frameworks, simulation algorithms, modeling formats, bio.tools |
is used by: runBioSimulations is listed by: bio.tools is listed by: Debian |
Center for Reproducible Biomodeling Modeling ; National Institute of Bioimaging and Bioengineering ; National Institute of General Medical Sciences ; National Institutes of Health ; National Science Foundation |
Free, Freely available | biotools:biosimulators | https://bio.tools/biosimulators | SCR_019111 | 2026-08-05 10:47:09 | 5 | |||||||
|
AmpliconTagger Resource Report Resource Website 1+ mentions |
AmpliconTagger (RRID:SCR_019112) | data processing software, software application, workflow software, software resource | Software tool as rRNA marker gene amplicon pipeline coded in python framework that enables fine tuning and integration of virtually any potential rRNA gene amplicon bioinformatic procedure. Designed to work within HPC environment, supporting complex network of job dependencies with smart restart mechanism in case of job failure or parameter modifications. | High Performance Computing, HPC environment, rRNA gene amplicons, rRNA marker, gene amplicon pipeline, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:31816087 | Free, Freely available | SCR_019113, biotools:amplicontagger | https://bitbucket.org/jtremblay514/nrc_pipeline_public/src/master/, https://jtremblay.github.io/amplicontagger_guide.html, https://bio.tolols/amplicontagger | SCR_019112 | 2026-08-05 10:47:10 | 3 |
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