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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CajaDB Resource Report Resource Website 1+ mentions |
CajaDB (RRID:SCR_016506) | data or information resource, database, software resource, web application | 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 ; Brain Institute ; Brazilian Council for Research and Technological Development ; Federal University of Rio Grande do Norte ; Multidisciplinary Environment ; NPAD/UFRN |
Free, Freely available | SCR_016506 | 2026-08-29 11:25:47 | 1 | ||||||||||
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DINIES Resource Report Resource Website 1+ mentions |
DINIES (RRID:SCR_016505) | DINIES | data analysis software, data processing software, sequence analysis software, software application, software resource, 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 | 2026-08-29 11:25:18 | 6 | ||||
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PNNsMiceMachineVision Resource Report Resource Website 1+ mentions |
PNNsMiceMachineVision (RRID:SCR_016485) | PNNsMiceMachineVision | data or information resource, database, software application, software resource, source code | 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 | 2026-08-29 11:25:15 | 2 | |||||||||
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MorphoJ Resource Report Resource Website 10+ mentions |
MorphoJ (RRID:SCR_016483) | data analysis software, data processing software, software application, 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 | 2026-08-29 11:25:18 | 38 | |||||||||
|
SABRe CVD Initiative Resource Report Resource Website |
SABRe CVD Initiative (RRID:SCR_016572) | SABRe CVD | data or information resource, disease-related portal, portal, topical portal | Project to generate extensive biomarker data from Framingham Heart Study participants using immunoassays, proteomics, metabolomics/lipomics, and gene expression and microRNA profiling to advance personalized medicine through biomarker discovery and validation. | generate, biomarker, discovery, data, Framingham, Heart, Study, gene, expression, omicdata | cardiovascular disease, atherosclerosis | Free, Partially available for public, Requested authorized access | SCR_016572 | Systems Approach to Biomarker Research in CardioVascular Disease | 2026-08-29 11:25:18 | 0 | ||||||||
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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, database, organism-related portal, portal, project portal, software resource, topical portal, web service | 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 | 2026-08-29 11:25:15 | 2 | |||||||||
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MentaLiST Resource Report Resource Website 10+ mentions |
MentaLiST (RRID:SCR_016469) | data analysis software, data processing software, sequence analysis software, software application, software resource | 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 BC ; Genome Canada |
PMID:29319471 | Free, Available for download, Freely available | biotools:mentalist | https://bio.tools/mentalist | SCR_016469 | 2026-08-29 11:25:45 | 15 | ||||||
|
cisTEM Resource Report Resource Website 50+ mentions |
cisTEM (RRID:SCR_016502) | cisTEM | data processing software, image processing software, software application, 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 | 2026-08-29 11:25:16 | 67 | ||||
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Calliope calcium imaging processing package Resource Report Resource Website 1+ mentions |
Calliope calcium imaging processing package (RRID:SCR_021213) | data processing software, image processing software, software application, software resource, software toolkit | Software package for image processing for MATLAB. Used for processing of calcium imaging data. | Image processing, data, calcium imaging data, calcium imaging |
is used by: IRIS two photon acquisition package is related to: MATLAB |
Novartis Research Foundation ; Swiss National Science Foundation |
DOI:10.1016/j.cell.2017.05.023 | Free, Available for download, Freely available | SCR_021213 | 2026-08-29 11:27:06 | 1 | ||||||||
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Cumulus Resource Report Resource Website 1+ mentions |
Cumulus (RRID:SCR_021644) | data analysis software, data processing software, software application, software resource | Software tool as cloud based single cell genomics and spatial transcriptomics data analysis framework that is scalable to massive amounts of data and able to process variety of data types. Consists of cloud analysis workflow, Python analysis package and visualization application. Supports analysis of single-cell RNA-seq, CITE-seq, Perturb-seq, single-cell ATAC-seq, single-cell immune repertoire and spatial transcriptomics data. | Single cell genomics, spatial transcriptomics, single-cell RNA-seq, CITE-seq, Perturb-seq, single-cell ATAC-seq, single-cell immune repertoire, data |
uses: Pegasus uses: Cirrocumulus uses: Pegasus-fus is listed by: Terra is related to: BICCN has parent organization: Broad Institute |
Frederick National Laboratory for Cancer Research ; HHMI ; Klarman Cell Observatory ; Leidos Biomedical Research ; Ludwig Center at MIT ; Manton Foundation ; NCI |
DOI:10.1038/s41592-020-0905-x | Free, Available for download, Freely available | https://app.terra.bio/#workspaces/kco-tech/Cumulus, https://github.com/klarman-cell-observatory/cumulus/blob/91336094646217564a4f8e7b31c03c3c6bf2e84b/docs/index.rst | SCR_021644 | 2026-08-29 11:27:14 | 3 | |||||||
|
Stan Resource Report Resource Website 100+ mentions |
Stan (RRID:SCR_018459) | programming language, simulation software, software application, software resource | Probabilistic programming language for specifying statistical models. Defines log probability function over parameters conditioned on specified data and constants. Platform for statistical modeling and high performance statistical computation. Provides full Bayesian inference for posterior expectations including parameter estimation and posterior predictive inference by defining appropriate derived quantities of interest. | Statistical model specification, statistical modeling, statistical computation, log probability function, parameter, data, constant, parameter estimation | DOI:1509.07164 DOI:10.18637/jss.v076.i01 |
Free, Available for download, Freely available | SCR_018459 | 2026-08-29 11:26:08 | 221 | ||||||||||
|
ReproNim/containers Resource Report Resource Website 1+ mentions |
ReproNim/containers (RRID:SCR_018467) | data or information resource, knowledge environment resource, narrative resource, portal, software resource, software toolkit, training material, workflow | Software containerized environments for reproducible neuroimaging. Part of ReproNim - Center for Reproducible Neuroimaging Computation. DataLad dataset with collection of popular computational tools provided within ready to use containerized environments. | Containerized environment, reproducible neuroimaging, ReproNim, neuroimaging, dataset, DataLad, imaging, data | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | German Federal Ministry of Education and Research ; NIBIB P41 EB019936; NSF 1429999 |
Free, Freely available | https://github.com/ReproNim/containers | SCR_018467 | 2026-08-29 11:25:46 | 1 | ||||||||
|
ggtree Resource Report Resource Website 50+ mentions |
ggtree (RRID:SCR_018560) | data processing software, data visualization software, software application, software resource | Software R package for visualization and annotation of phylogenetic trees with their covariates and other tree like structures with their annotation data. Can import evolutionary data from different tree file formats and analysis programs as well as other associated data from experiments so that various sources and types of data can be displayed on tree for comparison and further analyses. | Phylogenetic tree visualization, phylogenetic tree annotation, data, bio.tools |
is listed by: CRAN is listed by: Bioconductor is listed by: Debian is listed by: bio.tools |
Seed Funding Programme for Basic Research | DOI:10.1111/2041-210X.12628 | Free, Available for download, Freely available | biotools:ggtree | https://bio.tools/ggtree | SCR_018560 | 2026-08-29 11:25:47 | 61 | ||||||
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DAMBE Resource Report Resource Website 10+ mentions |
DAMBE (RRID:SCR_018528) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software package for data analysis in molecular biology and evolution. Integrated software package for converting, manipulating, statistically and graphically describing, and analyzing molecular sequence data. Used for genomic and phylogenetic data analysis on Windows, Linux, and Macintosh computers. | Data analysis, molecular sequence data, genomic data, phylogenetic data, data, anaysis, sequence analysis, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Ottawa; Ontario; Canada |
Hong Kong Research Grant Council ; Natural Science and Engineering Research Council of Canada ; University of Hong Kong |
PMID:11535656 PMID:28379490 PMID:23564938 PMID:29669107 |
Free, Available for download, Freely available | biotools:dampe | https://bio.tools/dambe | SCR_018528 | DAMBE6, DAMBE5, DAMBE7, Data Analysis in Molecular Biology and Evolution | 2026-08-29 11:26:09 | 12 | |||||
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Machado Resource Report Resource Website 1+ mentions |
Machado (RRID:SCR_018428) | application programming interface, data access protocol, data or information resource, software resource, web service | Software tool as framework to store, search and visualize biological data. Django instance provides data management, visualization, and searching functionalities to Chado databases. Resulting object-relational framework enables users, not only to set up local instance containing data regarding their organisms of interest, but also to develop all sorts of tools by accessing open source code. | Python, genomics, data, framework, data visualization, data management, Chado datbase, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Plant Co-expression Annotation Resource |
Embrapa | Free, Available for download, Freely available | biotools:machado | https://bio.tools/machado | SCR_018428 | 2026-08-29 11:26:08 | 2 | |||||||
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CohortMethod Resource Report Resource Website 10+ mentions |
CohortMethod (RRID:SCR_018511) | data analysis software, data processing software, data visualization software, software application, software resource | Software R package for performing new user cohort studies in observational database in OMOP Common Data Model. | Cohort study, observational database, OMOP Common Data Model, data, drugs, diagnosis, procedure, age, comorbidity index, data visualization | NSF IIS 1251151 | Free, Available for download, Freely available | SCR_018511 | 2026-08-29 11:26:08 | 11 | ||||||||||
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piNET Resource Report Resource Website 1+ mentions |
piNET (RRID:SCR_018693) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web platform for downstream analysis and visualization of proteomics data. Server that facilitates integrated annotation, analysis and visualization of quantitative proteomics data, with emphasis on PTM networks and integration with LINCS library of chemical and genetic perturbation signatures in order to provide further mechanistic and functional insights. Primary input for server consists of set of peptides or proteins, optionally with PTM sites, and their corresponding abundance values. | Analysis, visualization, proteomics data, integrated annotation, quantitative proteomics data, PTM network, LINCS library integration, genetic perturbation signature, peptide, protein, post translational modification site, PTM site, data | is related to: LINCS Project | NCATS UL1 TR001425; NCI T32 CA236764; NHLBI U54 HL127624; NIEHS P30 ES006096; NIGMS U01 GM120953; NIMH R01 MH107487 |
DOI:10.1093/nar/gkaa436 | Free, Freely available | SCR_018693 | 2026-08-29 11:25:50 | 4 | ||||||||
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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 | 2026-08-29 11:25:55 | 7 | |||||||
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Toolbox for Representational Similarity Analysis Resource Report Resource Website 1+ mentions |
Toolbox for Representational Similarity Analysis (RRID:SCR_019029) | data analysis software, data processing software, software application, software resource, software toolkit | Software Matlab toolbox to perform representational similarity analysis for neural data. | Representional similarity analysis, data analysis, data, neural data |
is related to: MATLAB has parent organization: University of Cambridge; Cambridge; United Kingdom |
European Research Council Advanced Grant ; European Research Council Starting Grant ; UK Medical Research Council |
PMID:24743308 | Free, Available for download, Freely available | SCR_019029 | RSA toolbox | 2026-08-29 11:26:17 | 9 | |||||||
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CLIP Tool Kit Resource Report Resource Website 10+ mentions |
CLIP Tool Kit (RRID:SCR_019034) | CTK | data analysis software, data processing software, software application, software resource, software toolkit | Software package that provides set of tools for analysis of CLIP data starting from raw reads generated by sequencer. | CLIP data, data analysis, raw reads, sequencer data generation, genome assemblies, data | has parent organization: Columbia University; New York; USA | Free, Available for download, Freely available | SCR_019034 | 2026-08-29 11:26:18 | 22 |
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