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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
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 | 2026-02-16 09:49:39 | 129 | ||||||
|
EnteroBase Resource Report Resource Website 100+ mentions |
EnteroBase (RRID:SCR_019019) | web service, data access protocol, database, software resource, data or information resource | 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 | 2026-02-16 09:49:37 | 233 | |||||||
|
D-GENIES Resource Report Resource Website 10+ mentions |
D-GENIES (RRID:SCR_018967) | software application, data processing software, image analysis software, software resource, web application, alignment software, standalone software | 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 | 2026-02-16 09:49:34 | 46 | ||||||
|
Robetta Resource Report Resource Website 100+ mentions |
Robetta (RRID:SCR_018805) | web service, data access protocol, analysis service resource, software resource, production service resource, service resource | 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 | 2026-02-16 09:49:34 | 330 | |||||||
|
NanoGalaxy Resource Report Resource Website 1+ mentions |
NanoGalaxy (RRID:SCR_018912) | software application, data processing software, software toolkit, web service, data visualization software, data analysis software, data access protocol, software resource | 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 | 2026-02-16 09:49:35 | 9 | ||||||||
|
BadMedicine Resource Report Resource Website 1+ mentions |
BadMedicine (RRID:SCR_018879) | software development tool, software application, software toolkit, software library, software resource, code testing framework | 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 | 2026-02-16 09:49:32 | 1 | ||||||||
|
fracridge Resource Report Resource Website 1+ mentions |
fracridge (RRID:SCR_019045) | software application, data processing software, data analysis software, 1d time-series analysis software, 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 | 2026-02-16 09:49:38 | 1 | |||||||
|
ScanITD Resource Report Resource Website 1+ mentions |
ScanITD (RRID:SCR_018886) | software application, data processing software, 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 | 2026-02-16 09:49:35 | 1 | |||||
|
TRiCoLOR Resource Report Resource Website 1+ mentions |
TRiCoLOR (RRID:SCR_018801) | software application, data processing software, 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 | 2026-02-16 09:49:35 | 2 | ||||||||
|
STAMP Resource Report Resource Website 500+ mentions |
STAMP (RRID:SCR_018887) | software application, data processing software, software toolkit, data visualization software, data analysis software, 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 | 2026-02-16 09:49:36 | 504 | |||||
|
SynergyFinder Resource Report Resource Website 500+ mentions |
SynergyFinder (RRID:SCR_019318) | software application, data processing software, software toolkit, data visualization software, software resource | Software R package as efficient implementations for all popular synergy scoring models for drug combinations, including HSA, Loewe, Bliss and ZIP and visualization of synergy scores as either two dimensional or three dimensional interaction surface over dose matrix. Used to calculate and visualize synergy scores for drug combinations. | Synergy scores, drug combinations, popular synergy scoring models, dimensional interaction surface, dose matrix, bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is related to: SynergyFinder web application |
DOI:10.1007/978-1-4939-7493-1_17 | Free, Available for download, Freely available | biotools:synergyfinder | https://bio.tools/synergyfinder | SCR_019318 | synergyfinder | 2026-02-16 09:49:39 | 510 | ||||||
|
Omics Data Paper Generator Resource Report Resource Website 1+ mentions |
Omics Data Paper Generator (RRID:SCR_019809) | software development tool, software application, data processing software, web service, documentation generation software, data access protocol, software resource, workflow software | Software package for streamlined import of omics metadata from European Nucleotide Archive into OMICS Data Paper manuscript. Omics Data Paper R Shiny app demonstrates workflow for automatic import of ENA genomic metadata into omics data paper manuscript. Streamlined conversion of metadata into manuscript facilitates authoring of omics data papers, which allow omics dataset creators to receive credit for their work and to improve description and visibility of their datasets. | Workflow, genomics, omics, FAIR data, data paper, G Power, European Nucleotide Archive, genomic metadata, omics data paper manuscript, streamlined conversion, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Shiny |
Horizon 2020 764840 | Free, Available for download, Freely available | biotools:omics-data-paper-shinyapp-golem | https://mdmtrv.shinyapps.io/Omics_data_paper/ https://bio.tools/omics-data-paper-shinyapp-golem |
SCR_019809 | omicsdatapaper | 2026-02-16 09:49:43 | 1 | ||||||
|
Parliament2 Resource Report Resource Website 1+ mentions |
Parliament2 (RRID:SCR_019187) | software application, data processing software, software toolkit, data analysis software, 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 | 2026-02-16 09:49:41 | 5 | ||||||||
|
epitopepredict Resource Report Resource Website 1+ mentions |
epitopepredict (RRID:SCR_019221) | software application, software resource, simulation software | Open source software tool as programmatic framework and command line tool designed to aid process of MHC binding prediction. Provides access to multiple binding prediction algorithms under single interface and scales for whole genomes using multiple target MHC alleles.Software should be run on Linux operating system. Ubuntu is recommended but most major distributions will be fine. Windows is not supported. | Protein sequence, MHC binding prediction, whole genomes, multiple target MHC allele, epitope prediction, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:epitopepredict | https://epitopepredict.readthedocs.io/en/latest/ https://bio.tools/epitopepredict |
SCR_019221 | 2026-02-16 09:49:39 | 2 | ||||||||
|
long-read-tools Resource Report Resource Website 10+ mentions |
long-read-tools (RRID:SCR_019116) | software repository, data or information resource, database, software resource | 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 | 2026-02-16 09:49:40 | 11 | ||||||
|
AmpliconTagger Resource Report Resource Website 1+ mentions |
AmpliconTagger (RRID:SCR_019112) | data processing software, software application, software resource, workflow software | 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 | 2026-02-16 09:49:36 | 3 | |||||||
|
variancePartition Resource Report Resource Website 50+ mentions |
variancePartition (RRID:SCR_019204) | software application, data processing software, data analytics software, data analysis software, software resource | Software R package to quantify and interpret divers of variation in multilevel gene expression experiments.Provides statistical and visualization framework for studying drivers of variation in RNA-seq datasets in many types of high throughput genomic assays including RNA-seq gene-, exon- and isoform-level quantification, splicing efficiency, protein quantification, metabolite quantification, metagenomic assays, methylation arrays and epigenomic sequencing assays. | Repeated measures, variation in gene expression, RNA-seq datasets, high throughput genomic assays, splicing efficiency, protein quantification, metabolite quantification, metagenomic assays, methylation arrays, epigenomic sequencing assays, bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is related to: CRAN |
NHLBI U01 HL107388; Icahn School of Medicine at Mount Sinai |
PMID:27884101 | Free, Available for download, Freely available | biotools:variancepartition | https://bio.tools/variancepartition | SCR_019204 | 2026-02-16 09:49:39 | 52 | ||||||
|
MP3 tool Resource Report Resource Website 1+ mentions |
MP3 tool (RRID:SCR_019282) | software application, software resource, simulation software | Software tool for prediction of pathogenic proteins in genomic and metagenomic data. Used for identification of partial pathogenic proteins predicted from short (100-150 bp) metagenomic reads and also performs on complete protein sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | pathogenic proteins, pathogenic proteins prediction, genomic data, metagenomic data, partial pathogenic proteins, partial pathogenic proteins prediction, complete protein sequences, bio.tools |
is listed by: bio.tools is listed by: Debian |
Institutional Research Fund of IISER Bhopal | PMID:24736651 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:mp3 | https://bio.tools/mp3 | SCR_019282 | MP3 | 2026-02-16 09:49:42 | 2 | |||||
|
Bs-Seeker2 Resource Report Resource Website 1+ mentions |
Bs-Seeker2 (RRID:SCR_020948) | software application, data processing software, sequence analysis software, data analysis software, software resource | Software tool as versatile aligning pipeline for bisulfite sequencing data. Used for mapping bisulfite sequencing data and generating DNA methylomes. Improves mappability over existing aligners by using local alignment. Maps reads from RRBS library by building special indexes with improved efficiency and accuracy. Provides additional function for filtering out reads with incomplete bisulfite conversion, which is useful in minimizing overestimation of DNA methylation levels. | Versatile aligning pipeline, bisulfite sequencing data, mapping bisulfite sequencing data, generating DNA methylomes, DNA methylation level, reads mapping, Reduced Represented Bisulfite Sequencing library, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: BS Seeker has parent organization: University of California at Los Angeles; California; USA |
Institute of Genomics and Proteomics at UCLA ; NBRPC 2012CB316503; China Scholarship Council |
PMID:24206606 | Free, Available for download, Freely available | biotools:bs-seeker2 | http://pellegrini.mcdb.ucla.edu/BS_Seeker2/ https://bio.tools/bs-seeker2 |
SCR_020948 | Bisulfite Sequencing Seeker2, BS Seeker2 | 2026-02-16 09:49:54 | 2 | |||||
|
ChiRA Resource Report Resource Website 1+ mentions |
ChiRA (RRID:SCR_019219) | software application, software toolkit, data processing software, narrative resource, workflow, training material, software resource, data or information resource | Software tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc. | RNA-RNA interactome experimental data, experimental data analysis, miRNA, RNA-RNA interactome, RNA structurome, CLASH, CLEAR-CLIP, PARIS, SPLASH, chimeric read, read, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:chira | https://rna.usegalaxy.eu/ https://bio.tools/chira |
SCR_019219 | Chimeric Read Analyzer | 2026-02-16 09:49:38 | 4 |
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