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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ObjTables Resource Report Resource Website |
ObjTables (RRID:SCR_018652) | data management software, data processing software, software application, software resource, software toolkit | 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; NIGMS R35 GM119771; NSF 1649014 |
Free, Freely available | biotools:objtables | https://bio.tools/objtables | SCR_018652 | 2026-09-12 12:59:04 | 0 | |||||||
|
Preseq Resource Report Resource Website 10+ mentions |
Preseq (RRID:SCR_018664) | data analysis software, data processing software, software application, software resource, software toolkit | 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 | 2026-09-12 12:59:04 | 21 | |||||||
|
minet Resource Report Resource Website |
minet (RRID:SCR_018661) | data analysis software, data processing software, network analysis software, software application, software resource, software toolkit | 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 | 2026-09-12 12:59:04 | 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 |
NCATS UL1 TR001114; NCI K22 CA188163; NHGRI U01 HG006476; NHGRI U01 HG008473; NIGMS GM083924; NIGMS U54 GM114833; 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 | 2026-09-12 12:59:04 | 34 | ||||||
|
TRACESPipe Resource Report Resource Website 1+ mentions |
TRACESPipe (RRID:SCR_018831) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool as hybrid pipeline for reconstruction and analysis of viral and host genomes at multi-organ level. Pipeline for identification, assembly, and analysis of viral genomes, that combine DNA sequence data from multiple organs. Cooperation between compression based prediction, sequence alignment, and de-novo assembly. Provides transmission and storage of data. | Hybrid pipeline, genome reconstruction, genome analysis, viral genome, host genome, multi organ sequencing, multi organ level, DNA sequence data, multiple organ data, bio.tools |
is listed by: bio.tools is listed by: Debian |
DOI:10.5524/100771 | Free, Freely available | biotools:tracespipe | http://dx.doi.org/10.5524/100771, https://bio.tools/tracespipe | SCR_018831 | 2026-09-12 12:59:06 | 2 | |||||||
|
Robetta Resource Report Resource Website 100+ mentions |
Robetta (RRID:SCR_018805) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web tool as protein structure prediction service. Provides automated structure prediction and analysis tools that can be used to infer protein structural information from genomic data. Produces model for entire protein sequence in presence or absence of sequence homology to protein of known structure. | Protein structure prediction, protein, structure prediction, prediction service, automated prediction, analysis tools, genomic data, protein sequence, protein model, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Washington; Seattle; USA |
PMID:15215442 | Restricted | biotools:robetta | https://bio.tools/robetta | SCR_018805 | 2026-09-12 12:59:06 | 487 | |||||||
|
ODAM Resource Report Resource Website 1+ mentions |
ODAM (RRID:SCR_018774) | data access protocol, data management software, 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 | 2026-09-12 12:59:05 | 3 | |||||||
|
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 | 2026-09-12 12:59:06 | 94 | ||||||
|
NanoGalaxy Resource Report Resource Website 10+ mentions |
NanoGalaxy (RRID:SCR_018912) | data access protocol, data analysis software, data processing software, data visualization software, software application, software resource, software toolkit, 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 | 2026-09-12 12:59:07 | 10 | ||||||||
|
BadMedicine Resource Report Resource Website 1+ mentions |
BadMedicine (RRID:SCR_018879) | code testing framework, software application, software development tool, software library, software resource, software toolkit | 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 | 2026-09-12 12:59:06 | 1 | ||||||||
|
ScanITD Resource Report Resource Website 1+ mentions |
ScanITD (RRID:SCR_018886) | data analysis software, data processing software, sequence analysis software, software application, 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 | 2026-09-12 12:59:07 | 1 | |||||
|
TRiCoLOR Resource Report Resource Website 1+ mentions |
TRiCoLOR (RRID:SCR_018801) | data analysis software, data processing software, sequence analysis software, software application, 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 | 2026-09-12 12:59:06 | 2 | ||||||||
|
STAMP Resource Report Resource Website 500+ mentions |
STAMP (RRID:SCR_018887) | data analysis software, data processing software, data visualization software, software application, software resource, software toolkit | 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 |
Australian Research Council ; Canada Foundation for Innovation ; Canada Research Chairs program ; Dalhousie Centre for Comparative Genomics and Evolutionary Bioinformatics ; Dalhousie Faculty of Computer Science ; Genome Atlantic ; Natural Sciences and Engineering Research Council of Canada ; 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 | 2026-09-12 12:59:07 | 588 | |||||
|
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 |
NHGRI R24 HG010032; NIAID U19 AI118610; NIAID U19 AI118626; NIGMS ; NIH Common Fund |
PMID:30526489 | biotools:GOnet | https://github.com/mikpom/gonet, https://bio.tools/GOnet | SCR_018977 | 2026-09-12 12:59:08 | 7 | |||||||
|
E-CRISP Resource Report Resource Website 100+ mentions |
E-CRISP (RRID:SCR_019088) | data access protocol, software resource, web service | Web application to design gRNA sequences. Uses algorithms to identify sgRNA target sequences in any nucleotide sequence for use in CRISPR/Cas mediated genome editing. Used for fast CRISPR target site identification. Enables designing of multiple libraries and creates genome scale libraries for several organisms in few hours. | gRNA sequence design, sgRNA target sequence identification, CRISPR, CRISPR/Cas mediated genome editing, library design, multiple libraries, genome scale libraries, bio.tools |
is listed by: Debian is listed by: bio.tools |
European Research Council Advanced Grant of the European Commission | PMID:24481216 | Free, Freely available | biotools:e-crisp | https://bio.tools/e-crisp | SCR_019088 | 2026-09-12 12:59:09 | 147 | ||||||
|
EnteroBase Resource Report Resource Website 100+ mentions |
EnteroBase (RRID:SCR_019019) | data access protocol, data or information resource, database, software resource, 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 | 2026-09-12 12:59:08 | 317 | |||||||
|
D-GENIES Resource Report Resource Website 50+ mentions |
D-GENIES (RRID:SCR_018967) | alignment software, data processing software, image analysis software, software application, software resource, standalone software, web application | 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 | 2026-09-12 12:59:08 | 56 | ||||||
|
fracridge Resource Report Resource Website 1+ mentions |
fracridge (RRID:SCR_019045) | 1d time-series analysis software, data analysis software, data processing software, software application, software resource, time-series analysis software | Software tool as regularization technique that penalizes L2-norm of coefficients in linear regression. Available in two programming languages MATLAB and Python. | Generalized linear model, hyperparameters, regularization technique, coefficient, linear regression, L2 norm, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:fracridge | https://bio.tools/fracridge | SCR_019045 | fractional ridge regression | 2026-09-12 12:59:09 | 1 | |||||||
|
BiG-SLiCE Resource Report Resource Website 1+ mentions |
BiG-SLiCE (RRID:SCR_019130) | data analysis software, data processing software, software application, software resource | 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 |
Graduate School for Experimental Plant Sciences Netherlands ; Netherlands eScience Center Accelerating Scientific Discoveries Grant |
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 | 2026-09-12 12:59:10 | 6 | |||||
|
Parliament2 Resource Report Resource Website 1+ mentions |
Parliament2 (RRID:SCR_019187) | data analysis software, data processing software, software application, software resource, software toolkit | 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 | 2026-09-12 12:59:10 | 5 |
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