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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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long-read-tools Resource Report Resource Website 10+ mentions |
long-read-tools (RRID:SCR_019116) | software resource, database, data or information resource, software repository | 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 | 2026-08-04 09:44:29 | 11 | ||||||
|
runBioSimulations Resource Report Resource Website 1+ mentions |
runBioSimulations (RRID:SCR_019110) | web application, software resource | 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 | 2026-08-04 09:44:32 | 3 | |||||||
|
BioSimulators Resource Report Resource Website 1+ mentions |
BioSimulators (RRID:SCR_019111) | web application, software resource, software repository | 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 | 2026-08-04 09:44:29 | 5 | |||||||
|
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 | 2026-08-04 09:44:29 | 3 | |||||||
|
variancePartition Resource Report Resource Website 50+ mentions |
variancePartition (RRID:SCR_019204) | data processing software, data analysis software, software resource, software application, data analytics software | 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 | 2026-08-04 09:44:34 | 52 | ||||||
|
fracridge Resource Report Resource Website 1+ mentions |
fracridge (RRID:SCR_019045) | data processing software, data analysis software, time-series analysis software, software resource, software application, 1d 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 | 2026-08-04 09:44:28 | 1 | |||||||
|
ChiRA Resource Report Resource Website 1+ mentions |
ChiRA (RRID:SCR_019219) | data processing software, workflow, software resource, training material, software application, narrative resource, software toolkit, 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 | 2026-08-04 09:44:31 | 4 | |||||||
|
SynergyFinder Resource Report Resource Website 500+ mentions |
SynergyFinder (RRID:SCR_019318) | data processing software, software resource, software application, data visualization software, software toolkit | 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 | 2026-08-04 09:44:35 | 510 | ||||||
|
fgsea Resource Report Resource Website 100+ mentions |
fgsea (RRID:SCR_020938) | data processing software, software application, software resource, data analysis software | Software R package for fast preranked gene set enrichment analysis. Allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. | Gene set enrichment analysis, preranked gene set, multiple hypothesis correction, bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian |
DOI:10.1101/060012 | Free, Available for download, Freely available | biotools:fgsea | https://github.com/ctlab/fgsea/, https://bio.tools/fgsea | SCR_020938 | fast gene set enrichment analysis, Fast Gene Set Enrichment Analysis, FGSEA | 2026-08-04 09:44:41 | 185 | ||||||
|
Omics Data Paper Generator Resource Report Resource Website 1+ mentions |
Omics Data Paper Generator (RRID:SCR_019809) | data processing software, software development tool, web service, software resource, documentation generation software, data access protocol, software application, 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 | 2026-08-04 09:44:36 | 1 | ||||||
|
CiteFuse Resource Report Resource Website 1+ mentions |
CiteFuse (RRID:SCR_019321) | data processing software, software application, software resource, data analysis software | Software R package consisting of suite of tools for doublet detection, modality integration, clustering, differential RNA and protein expression analysis, antibody-derived tag evaluation, ligand-receptor interaction analysis and interactive web-based visualization of CITE-seq data. | Data pre processing, modality integration, clustering, differential RNA, ADT, expression analysis, ADT evaluation, ligand receptor interaction analysis, CITE-seq data, cellular indexing of transcriptomes and epitopes by sequencing, bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian has parent organization: University of Sydney; Sydney; Australia |
PMID:32353146 | Free, Available for download, Freely available | biotools:citefuse | https://bioconductor.org/packages/CiteFuse/, https://github.com/SydneyBioX/CiteFuse/, http://shiny.maths.usyd.edu.au/CiteFuse/, https://bio.tools/CiteFuse | SCR_019321 | Cellular Indexing of Transcriptomes and Epitopes Fuse, Cellular indexing of transcriptomes and epitopes Fuse | 2026-08-04 09:44:33 | 2 | ||||||
|
MP3 tool Resource Report Resource Website 1+ mentions |
MP3 tool (RRID:SCR_019282) | simulation software, software application, software resource | 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 | 2026-08-04 09:44:35 | 2 | |||||
|
Bs-Seeker2 Resource Report Resource Website 1+ mentions |
Bs-Seeker2 (RRID:SCR_020948) | data processing software, data analysis software, software resource, sequence analysis software, software application | 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 | 2026-08-04 09:44:41 | 2 | |||||
|
BLINK Resource Report Resource Website 1+ mentions |
BLINK (RRID:SCR_016288) | data processing software, data analysis software, algorithm resource, software resource, software application | Software for next level of genome wide association studies with both individuals and markers in millions. The method releases the requirement that causative genes are evenly distributed on genome and consequently boosts statistical power. | GWAS, SNP, dataset, r, genome, bayesian, linkage, nested, keyway, statistic, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Tutorial available | biotools:BLINK | https://bio.tools/BLINK | SCR_016288 | BLINK (Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway) | 2026-08-04 09:43:51 | 1 | |||||||
|
SMAGEXP Resource Report Resource Website 1+ mentions |
SMAGEXP (RRID:SCR_016360) | SMAGEXP | data processing software, data analysis software, software resource, software application, software toolkit | Software toolkit for transcriptomics data meta-analysis. It integrates metaMA and metaRNAseq packages into Galaxy, carries out meta-analysis of gene expression data, handles microarray data from Gene Expression Omnibus (GEO) database, and more. | transcriptomics, data, meta, analysis, MicroArrays, RNA-Seq, Galaxy, gene, expression, next, generation, sequencing, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Galaxy is related to: Gene Expression Omnibus is related to: metaMA is related to: metaRNASeq |
PMID:30698691 | Free, Available for download, Freely available | biotools:SMAGEXP | https://bio.tools/SMAGEXP | SCR_016360 | Statistical Meta Analysis for Gene EXPression | 2026-08-04 09:43:53 | 2 | |||||
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FluxModeCalculator Resource Report Resource Website 1+ mentions |
FluxModeCalculator (RRID:SCR_016290) | data processing software, software application, software resource, data analysis software | Software for performing flux mode analysis in stoichiometric models. FluxModeCalculator enables large-scale elementary flux mode (EFM) computation and uses the OpenMP API to optimally exploit processor architectures with multiple cores., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | efm, flux, stoichiometry, algorithm, matlab, linux, model, magnitude, bio.tools |
is listed by: Debian is listed by: bio.tools |
Netherlands Consortium for Systems Biology (NCSB) ; Center of Medical Systems Biology (CMSB) ; European Network for Genetic and Genomic Epidemiology (ENGAGE) ; Biobanking and Biomolecular Resources Research Infrastructure (BBMRI) ; CardioVascular Research Netherlands (CVON-ENERGISE) |
PMID:26685305 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:fluxmodecalculator, OMICS_10894 | https://bio.tools/fluxmodecalculator | SCR_016290 | Flux Mode Calculator | 2026-08-04 09:43:52 | 1 | |||||
|
Lifebit Deploit Resource Report Resource Website 1+ mentions |
Lifebit Deploit (RRID:SCR_016428) | data analysis service, analysis service resource, data management software, software resource, software application, production service resource, service resource | Platform for computing management for data analysis on the cloud from the Lifebit company. Allows the computational analyses to be permanently linked to live analyses pipelines. | Lifebit, compute, management, data, analysis, cloud, integrate, data, reproduce, transparent, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:28398311 | Commercially available | biotools:nextflow | https://bio.tools/nextflow | SCR_016428 | 2026-08-04 09:43:53 | 2 | |||||||
|
Microscopy Image Browser Resource Report Resource Website 100+ mentions |
Microscopy Image Browser (RRID:SCR_016560) | MIB | data processing software, data analysis software, standalone software, software resource, software application, image processing software, data visualization software | Software package for advanced image processing, analysis, segmentation and visualization of multi-dimensional (2D-4D) light and electron microscopy datasets. | segmentation, analysis, multidimentional, dataset, light, electron, microscopy, image, processing, visualization, data, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: MATLAB |
Biocenter Finland ; Biological Imaging Network Academy of Finland ; University of Helsinki |
PMID:26727152 | Free, Available for download, Freely available | biotools:mib | https://www.youtube.com/watch?v=I9FWmJX_nl0&index=1&list=PLGkFvW985wz8cj8CWmXOFkXpvoX_HwXzj, https://bio.tools/mib | SCR_016560 | MIB, Microscopy Image Browser | 2026-08-04 09:43:55 | 143 | ||||
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MetaCyto Resource Report Resource Website 1+ mentions |
MetaCyto (RRID:SCR_016415) | data processing software, data analysis software, software resource, software application, software toolkit | Software tool for automated meta-analysis of mass and flow cytometry data. Provides functions for preprocessing, automated gating and meta-analysis of cytometry data and collection of cytometry data from the ImmPort database. | automated, analysis, meta, flow, cytometry, data, bio.tools |
is listed by: Bioconductor is listed by: NIDDK Information Network (dkNET) is listed by: bio.tools is listed by: Debian is related to: The Immunology Database and Analysis Portal (ImmPort) |
the National Institute of Allergy and Infectious Diseases HHSN272201200028C | Free, Available for download, Freely available | biotools:metacyto | https://bio.tools/metacyto | SCR_016415 | 2026-08-04 09:43:54 | 5 | |||||||
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DINIES Resource Report Resource Website 1+ mentions |
DINIES (RRID:SCR_016505) | DINIES | data processing software, data analysis software, software resource, sequence analysis software, software application, web application | Web server for predicting unknown drug-target interaction networks from various types of biological data in the framework of supervised network inference. | predict, drug, target, interaction, network, biological, data, chemical, structure, protein, amino acid, sequence, domain, bio.tools |
is listed by: GenomeNet is listed by: Debian is listed by: bio.tools is related to: KEGG has parent organization: Kyoto University; Kyoto; Japan |
Ministry of Education ; Culture ; Sports ; Science and Technology of Japan ; the Japan Science and Technology Agency ; the Japan Society for the Promotion of Science |
PMID:24838565 | Free, Freely available | biotools:dinies | https://bio.tools/dinies | SCR_016505 | Drug target Interaction Network Inference Engine based on Supervised analysis | 2026-08-04 09:43:54 | 4 |
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