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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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BIOQUANT Life Science Resource Report Resource Website 10+ mentions |
BIOQUANT Life Science (RRID:SCR_016423) | software application, data processing software, data analysis software, software resource, software toolkit, image analysis software | Software tool to collect and analyse data on images of tissue slides or welled plates.Supports high-throughput immunofluorescence and immunohistochemistry, stereology, densitometry, and 3D modeling. Used in bioscience research in animal models and human biopsy, developmental neuroscience, traumatic brain/spinal cord injury, glaucoma, eye-movement disorders, cardiovascular disease and muscle disorders. | BioQuant Inc., collect, analyse, data, tissue, slide, well, plate, capture, camera, scanned, image, immunofluorescence, immunohistochemistry, stereology, densitometry, 3D modeling | Commercially available, Tutoring available | SCR_016423 | 2026-02-17 10:03:01 | 19 | |||||||||||
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CajaDB Resource Report Resource Website 1+ mentions |
CajaDB (RRID:SCR_016506) | data or information resource, database, web application, software resource | Software application as an integrated web resource of marmoset biological data. Used to find genomic, expression and alternative splicing data to facilitate the study of animal model for neuropsychiatric and social behavior research and to support biological analyses such as functional (ontology) enrichment analysis and protein-protein-network. | marmoset, data, genomic, expression, alternative, splicing, animal, model, neuropsychiatry, social, behavior, ontology, protein, network | Amazonas State Research Support Foundation ; Federal University of Rio Grande do Norte ; Brain Institute ; Multidisciplinary Environment ; NPAD/UFRN ; Brazilian Council for Research and Technological Development |
Free, Freely available | SCR_016506 | 2026-02-17 10:03:02 | 1 | ||||||||||
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DINIES Resource Report Resource Website 1+ mentions |
DINIES (RRID:SCR_016505) | DINIES | software application, web application, data processing software, data analysis software, software resource, sequence analysis software | 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 | 2026-02-17 10:03:27 | 4 | ||||
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Deeptools Resource Report Resource Website 1000+ mentions |
Deeptools (RRID:SCR_016366) | software application, data processing software, data analysis software, software resource, software toolkit, data visualization software | Python based tools to process, visualize and analyse high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq. Implemented within Galaxy framework. Used to perform complete bioinformatic workflows ranging from quality controls and normalizations of aligned reads to integrative analyses, including clustering and visualization approaches. | process, visualize, analysis, sequencing, data, ChIP-seq, RNA-seq, MNase-seq, quality, control, normalization, aligned, read, clustering, bioinformatic | works with: Galaxy | German Research Foundation SFB 992; German Epigenome Programme DEEP 01KU1216G |
PMID:27079975 | Free, Available for download, Freely available | http://deeptools.ie-freiburg.mpg.de/ | SCR_016366 | 2026-02-17 10:03:24 | 2418 | |||||||
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PNNsMiceMachineVision Resource Report Resource Website 1+ mentions |
PNNsMiceMachineVision (RRID:SCR_016485) | PNNsMiceMachineVision | software application, data or information resource, source code, database, software resource | Data and code (Python) related to research paper: V. Javier Traver, Filiberto Pla, Marta Miquel, Maria Carbo-Gas, Isis Gil-Miravet, Julian Guarque-Chabrera "Cocaine-induced preference conditioning: a machine vision perspective". | data, code, Phyton, research, paper, probabilistic, neural, network | Free, Available for download, Freely available | SCR_016485 | Probabilistic Neural Networks MiceMachineVision | 2026-02-17 10:03:25 | 2 | |||||||||
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MorphoJ Resource Report Resource Website 10+ mentions |
MorphoJ (RRID:SCR_016483) | software application, data processing software, data analysis software, software resource, software toolkit | Software package written in Java for geometric morphometric analysis for two- and three-dimensional landmark data. Offers user-friendly environment for standard multivariate analyses such as principal components, discriminant analysis and multivariate regression as well as specialized applications including phylogenetics, quantitative genetics and analyses of modularity in shape data. | geometric, morphometric, analyse, 2D, 3D, landmark, data, principal, component, discriminant, multivariate, regression, shape | has parent organization: University of Manchester; Manchester; United Kingdom | PMID:21429143 | Free, Available for download, Freely available | SCR_016483 | 2026-02-17 10:03:27 | 35 | |||||||||
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SMAGEXP Resource Report Resource Website 1+ mentions |
SMAGEXP (RRID:SCR_016360) | SMAGEXP | software application, data processing software, data analysis software, software resource, 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 | 2026-02-17 10:03:23 | 2 | |||||
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1000 Fungal Genome Project Resource Report Resource Website 1+ mentions |
1000 Fungal Genome Project (RRID:SCR_016463) | data access protocol, data or information resource, topical portal, project portal, database, software resource, web service, portal, organism-related portal | Web application to provide genomic information for fungi. Includes sequenced fungal genomes, those in progress, and selected nominations. Nomination of new species for genome sequencing in the families or only one reference genome possible after providing DNA/RNA samples for their sequencing. Used to explore the diversity of fungi important for energy and the environment. | project, genomic, information, fungi, data, sequence, energy, environment |
is related to: MycoCosm is related to: Lawrence Berkeley National Laboratory has parent organization: DOE Joint Genome Institute |
the DOE Office of Biological and Environmental Research (BER) | Free, Register for an account | SCR_016463 | 2026-02-17 10:02:42 | 2 | |||||||||
|
MentaLiST Resource Report Resource Website 1+ mentions |
MentaLiST (RRID:SCR_016469) | software application, data processing software, data analysis software, software resource, sequence analysis software | Software for a MLST (multi-locus sequence typing) caller, based on a k-mer counting algorithm and written in the Julia language. Designed and implemented to handle large typing schemes. | next, generation, sequencing, multi, locus, sequence, typing, pathogen, surveillance, gene, identify, strain, type, housekeeping, whole, genome, sequencing, data, bacteria, genotyping, bio.tools |
is listed by: bio.tools is listed by: Debian |
Canadian Institute for Health Research ; Genome Canada ; Genome BC |
PMID:29319471 | Free, Available for download, Freely available | biotools:mentalist | https://bio.tools/mentalist | SCR_016469 | 2026-02-17 10:03:27 | 8 | ||||||
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cisTEM Resource Report Resource Website 50+ mentions |
cisTEM (RRID:SCR_016502) | cisTEM | image processing software, software application, data processing software, software resource | Software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them. | data, processing, high, resolution, electron, cryo, macroscopy, single, particle, averaging, image, macromolecule, high, resolution, 3D, bio.tools |
is listed by: bio.tools is listed by: Debian |
Howard Hughes Medical Institute | DOI:10.7554/eLife.35383 | Open source, Trial available | biotools:cistem | https://bio.tools/cistem | SCR_016502 | computational imaging system for Transmission Electron Microscopy | 2026-02-17 10:03:02 | 64 | ||||
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Global Catalogue of Microorganisms Resource Report Resource Website 1+ mentions |
Global Catalogue of Microorganisms (RRID:SCR_016460) | GCM | data or information resource, topical portal, database, portal, organism-related portal | Database and information retrieval, analysis, and visualization system for microbial resources to help culture collections to manage, disseminate and share the information related to their holdings. Provides an interface for the scientific and industrial communities to access the microbial resource information. | research, deep, mining, genomic, data, retrival, analysis, visualisation, , microbial, resource, | the Strategic Priority Research Program of the Chinese Academy of Sciences ; the Bureau of International Cooperation of the Chinese Academy of Sciences ; the National Key Research Program of China ; the 13th Five-year Informatization Plan of the Chinese Academy of Sciences ; the National Science Foundation for Young Scientists of China |
PMID:29718202 | Free, Available to the scientific and industrial communities | r3d100010696 | https://doi.org/10.17616/R3J315 | SCR_016460 | GCM:Global Catalogue of Microorganisms | 2026-02-17 10:03:01 | 5 | |||||
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iMaps Resource Report Resource Website 1+ mentions |
iMaps (RRID:SCR_016705) | data or information resource, production service resource, analysis service resource, service resource, data analysis service, portal | Web server for analysis of high-resolution sequencing data. It can be used with all variants of CLIP,as well as with methods that interrogate RNA or DNA methylation, RNA processing, RNA structure or protein-DNA interactions. | Genialis, analysis, high-resolution, sequencing, data, RNA, DNA, protein, interaction |
is related to: iCount is related to: iCount |
Free, Registration required | SCR_016705 | 2026-02-17 10:03:27 | 9 | ||||||||||
|
Pavian Resource Report Resource Website 10+ mentions |
Pavian (RRID:SCR_016679) | web application, production service resource, analysis service resource, service resource, software resource, data analysis service | Software R package for interactive analysis of metagenomics classification results with a special focus on infectious disease diagnosis. Used for analyzing and visualization of metagenomics classification results from classifiers such as Kraken, Centrifuge and MetaPhlAn. Provides an alignment viewer for validation of matches to a particular genome. | interactive, analysis, metagenomics, classification, result, infectious, disease, diagnosis, data, visualization, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Centrifuge Classifier |
NHGRI R01 HG006677; NIGMS R01 GM083873; U. S. Army Research Office W911NF1410490 |
DOI:10.1101/084715 | Free, Freely available | biotools:pavian | https://fbreitwieser.shinyapps.io/pavian/ https://bio.tools/pavian |
SCR_016679 | 2026-02-17 10:03:04 | 22 | ||||||
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iCount Resource Report Resource Website 10+ mentions |
iCount (RRID:SCR_016712) | data analysis software, software application, data processing software, software resource | Software Python package for protein-RNA interaction analysis. Used for analysis of protein-RNA interactions with iCLIP sequencing data and RNA maps. | protein, RNA, interaction, analysis, iCLIP, sequencing, data, map |
is related to: iMaps is related to: iMaps |
Free, Available for download, Freely available, Tutorial available | https://icount.readthedocs.io/en/latest/ref_python.html https://hub.docker.com/r/tomazc/icount/ |
SCR_016712 | 2026-02-17 10:03:29 | 35 | |||||||||
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NeuroAnatomy Toolbox Resource Report Resource Website 1+ mentions |
NeuroAnatomy Toolbox (RRID:SCR_016716) | nat, NAT | data visualization software, software application, data processing software, data analysis software, software resource, image analysis software | Software R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons in the context of 3D brain structures. | biological, image, data, visualization, analysis, tracing, single, neuron, 3D, structure, brain |
is listed by: OMICtools is listed by: CRAN is related to: R Project for Statistical Computing is related to: elmr has parent organization: University of Cambridge; Cambridge; United Kingdom |
DOI:10.5281/zenodo.10171 | Free, Available for download, Freely available | https://cran.r-project.org/web/packages/nat/index.html |
SCR_016716 | NeuroAnatomy Toolbox, neuroanatomy toolbox, Neuro Anatomy Toolbox, neuro anatomy toolbox | 2026-02-17 10:02:45 | 5 | ||||||
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BD FACS Sortware sorter software Resource Report Resource Website 1+ mentions |
BD FACS Sortware sorter software (RRID:SCR_016722) | BD FACS Sortware software | software application, data processing software, data analysis software, software resource, data visualization software | Software to provide control of the cell sorter from configuration and compensation setup to acquisition, sorting, and analysis, making it easy to customize the instrument for specific applications. BD implements software solutions that integrate data, devices and systems. | control, cell, sorter, acquisition, analysis, integrate, data, instrument, system, Becton Dickinson and Company | Commercially available | SCR_016722 | , BD FACS Sortware, Becton Dickinson FACS Sortware, BD FACS Sortware software | 2026-02-17 10:02:45 | 5 | |||||||||
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VectorMap Resource Report Resource Website 10+ mentions |
VectorMap (RRID:SCR_016721) | data access protocol, storage service resource, data or information resource, database, service resource, software resource, web service, portal, data repository | Collection of disease maps, and mapped collection data and distribution models for arthropod disease vector species, including mosquitoes, ticks, sand flies, mites, and fleas, as well as the hosts/reservoirs of vector-borne disease pathogens. VectorMap is modeled after MosquitoMap. | disease, map, collection, data, distribution, model, arthropod, disease, vector, species | has parent organization: Walter Reed Biosystematics Unit | arthropod disease | US Department of Defense Global Emerging Infections Surveillance and Response System ; Division of the Armed Forces Health Surveillance Center ; Global Biodiversity Information System |
Public, Free, Available for download, Freely available, Acknowledgement requested, Tutorial available | SCR_016721 | 2026-02-17 10:03:27 | 22 | ||||||||
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Microscopy Image Browser Resource Report Resource Website 100+ mentions |
Microscopy Image Browser (RRID:SCR_016560) | MIB | software application, image processing software, standalone software, data processing software, data analysis software, software resource, 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 | 2026-02-17 10:03:28 | 143 | ||||
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SMI BeGaze Resource Report Resource Website 1+ mentions |
SMI BeGaze (RRID:SCR_016648) | SMI BeGaze | software application, standalone software, data processing software, data analysis software, software resource, software toolkit, data visualization software | Software package for eye tracking studies by New Bio Technology Ltd. Used for designing eye movement studies and recording, analyzing, visualizing data of eye tracking results. | eye, tracking, study, New Bio Technology Ltd, recording, analyzing, visualizing, data | Commercially available | SCR_016648 | SMI BeGaze™, SMI BehavioralGaze, SMI Behavioral and Gaze Analysis | 2026-02-17 10:03:28 | 7 | |||||||||
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circular statistics Resource Report Resource Website 10+ mentions |
circular statistics (RRID:SCR_016651) | CircStat | data analysis software, software application, data processing software, software resource | Software toolbox for MATLAB for the descriptive and inferential statistical analysis of directional data. | circular, inferential, statistics, directional, data |
has parent organization: Max Planck Institute for Biological Cybernetics; Tubingen; Germany works with: MATLAB |
German National Academic Foundation ; German Ministry of Education ; Science ; Research and Technology |
DOI:10.18637/jss.v031.i10 | Free, Available for download, Registration required to MathWorks Account, | https://github.com/circstat/circstat-matlab | SCR_016651 | Matlab Circular Statistics Toolbox, , circstat-matlab, circular statistics, Circular Statistics, CircStat for Matlab | 2026-02-17 10:03:27 | 42 |
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