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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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CRISPy-web Resource Report Resource Website 10+ mentions |
CRISPy-web (RRID:SCR_017970) | software resource, data access protocol, web service | Web tool to design sgRNAs for CRISPR applications. Web tool based on CRISPy to design sgRNAs for any user-provided microbial genome. Implemented as standalone web application for Cas9 target prediction. | Design, sgRNA, CRISP, microbial, genome, Cas9, target, prediction, data, guide, single, editing, bio.tools |
is listed by: bio.tools is listed by: Debian |
Novo Nordisk Foundation | PMID:29062934 | Free, Freely available | biotools:crispy | https://bio.tools/crispy | SCR_017970 | single guide RNA desing | 2026-07-28 09:44:40 | 25 | |||||
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VEnCode Resource Report Resource Website 1+ mentions |
VEnCode (RRID:SCR_018024) | VEnCode | software application, software resource, data analysis software, data processing software | Software tool to perform intersectional genetics-related operations to find VEnCodes using databases provided by FANTOM5 consortium, namely CAGE enhancer and transcription start site (TSS) databases. | FANTOM5 consortium, data, CAGE enhancer, transcription site database, intersectional genetics, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1101/552984 | Free, Available for download, Freely available | BioTools:VEnCode, biotools:VEnCode | https://bio.tools/VEnCode, https://bio.tools/VEnCode, https://bio.tools/VEnCode | SCR_018024 | Versatile Entry Codes | 2026-07-28 09:44:37 | 1 | |||||
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gProfiler2 Resource Report Resource Website 50+ mentions |
gProfiler2 (RRID:SCR_018190) | software application, software resource, data analysis software, data processing software | Software R interface to g:Profiler. Uses publicly available APIs of g:Profiler web tool which ensures that results from all of interfaces are consistent. Used for gene list functional enrichment analysis and namespace conversion. gprofiler2 package supports all the same organisms, namespaces and data sources as the web tool. | Gene list, functional enrichment analysis, namespace conversion, data, analysis |
is listed by: ELIXIR Tools and Data Services Registry is related to: R Project for Statistical Computing works with: g:Profiler |
Estonian Research Council grants ; European Regional Development Fund for CoE of Estonian ICT research EXCITE projects |
PMID:31066453 | Free, Available for download, Freely available | SCR_018190 | gprofiler2 | 2026-07-28 09:44:51 | 53 | |||||||
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QIIME 2 View Resource Report Resource Website 50+ mentions |
QIIME 2 View (RRID:SCR_018074) | software application, service resource, data processing software, software resource, data visualization software, data acquisition software | Web based serverless viewer of QIIME 2 artifacts and visualizations. Client side interface for viewing QIIME 2 artifacts and visualizations. Not needed working QIIME 2 installation to inspect QIIME 2 results. Supports viewing externally hosted files by automatically downloading and displaying them when links to files are provided. | QIIME 2, visualization, data, interface, file viewing, file download and displaying | Free, Freely available | https://github.com/qiime2/q2view | SCR_018074 | q2view | 2026-07-28 09:44:37 | 71 | |||||||||
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PremierBiosoft Proteo IQ Software Resource Report Resource Website 10+ mentions |
PremierBiosoft Proteo IQ Software (RRID:SCR_018072) | software application, data analysis software, software resource, data processing software, data analytics software | Software package as comprehensive qualitative and quantitative suite for proteomics. Used to validate and quantify proteins by combining results from popular mass spectrometry platforms and database search engines. Provides customizable interface to support any form of biological annotation. Used to compare protein quantitative results in relation to biological pathways, protein localization, protein function, or to transcript abundance. Every protein identification can be linked to any external or internal knowledge database. Custom links are provided to GenBank, UniProt, IPI, and SwissProt databases or in-house LIMS. | Proteomic, qualitative, quantitative, protein identification, data, PREMIER Biosoft, mass spectrometry data, database search engine |
works with: GenBank works with: UniProtKB works with: IPI |
Restricted | SCR_018072 | ProteoIQ | 2026-07-28 09:44:49 | 34 | |||||||||
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CircaDB Resource Report Resource Website 10+ mentions |
CircaDB (RRID:SCR_018078) | CircaDB | data or information resource, database, data access protocol, software resource, web service | Database of mammalian circadian gene expression profiles. Works with link outs to Wikipedia, HomoloGene, Refseq, etc.. Open source database of circadian transcriptional profiles from time course expression experiments from mice and humans. | Mammalian circadian gene, gene expression, expression profile, mice, human, gene annotation, data, time course expression data | PMID:23180795 | Free, Freely available | http://github.com/itmat/circadb | SCR_018078 | Circadian gene expression profiles DataBase | 2026-07-28 09:44:41 | 19 | |||||||
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QuB Resource Report Resource Website 1+ mentions |
QuB (RRID:SCR_018076) | QuB | software application, data analysis software, software resource, data processing software, software toolkit | Integrated software platform for ion channel biophysics and neurophysiology.Used to explore dynamics of hidden states in memoryless system. Open source software suite for solving kinetic models, for report generation with publishable graphics, function fitting and scripting for new and repeated processing and AD/DA I/O. Can be applied to any data modeled with Markov kinetics., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Ion channel biophysics, neurophysiology data, hiddent state, memoryless system, solving kinetic model, data, Markov kinetics, analysis | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_018076 | Quantify unknown Biophysics | 2026-07-28 09:44:49 | 2 | |||||||||
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Vivli Resource Report Resource Website 1000+ mentions |
Vivli (RRID:SCR_018080) | data or information resource, service resource, nonprofit organization | Independent, non-profit organization that has developed global data-sharing and analytics platform to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through creation and implementation of sustainable global data-sharing enterprise. Our focus is on sharing individual participant-level data from completed clinical trials. Users can search listed studies, request data sets from data contributors, aggregate data, or share data of their own. Vivli (Center for Clinical Research Data) is launching a portal to share participant-level data from COVID trials. | Global data sharing, clinical research data, data, sharing, analytical platform, clinical trial, COVID-19-related trials |
is used by: NIH Heal Project is recommended by: NIDDK Information Network (dkNET) is listed by: Data and Computational Resources to Address COVID-19 is listed by: re3data.org is listed by: DataCite is listed by: FAIRsharing |
COVID-19 | Doris Duke Charitable Foundation ; Leona M. and Harry B. Helmsley Charitable Trust ; Lyda Hill Philanthropies ; Phrma |
Restricted | DOI:10.17616/R3SB9S, DOI:10.25504/FAIRsharing.uovQrT, DOI:10.25934, r3d100012823 | https://vivli.org/vivli-covid-19-portal-2/, https://doi.org/10.17616/R3SB9S, https://doi.org/10.17616/r3sb9s, https://doi.org/10.25934/, https://dx.doi.org/10.25934/, https://fairsharing.org/10.25504/FAIRsharing.uovQrT, https://doi.org/10.17616/R3SB9S | SCR_018080 | 2026-07-28 09:44:37 | 1532 | ||||||
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MOON Resource Report Resource Website 1+ mentions |
MOON (RRID:SCR_018005) | software application, data analysis software, software resource, data processing software, software toolkit | Software package that autonomously diagnoses rare diseases from next generation sequencing NGS data using artificial intelligence by Diploid. | Diagnosis, rare disease, next generation sequencing, NGS, data, artificial intelligence, analysis, Diploid | Restricted | SCR_018005 | 2026-07-28 09:44:48 | 6 | |||||||||||
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Stan Resource Report Resource Website 100+ mentions |
Stan (RRID:SCR_018459) | software application, simulation software, programming language, 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 | 2026-07-28 09:44:41 | 173 | ||||||||||
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ReproNim/containers Resource Report Resource Website 1+ mentions |
ReproNim/containers (RRID:SCR_018467) | narrative resource, knowledge environment resource, data or information resource, software resource, workflow, software toolkit, portal, training material | 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) | NIBIB P41 EB019936; NSF 1429999; German Federal Ministry of Education and Research |
Free, Freely available | https://github.com/ReproNim/containers | SCR_018467 | 2026-07-28 09:44:57 | 1 | ||||||||
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MS Amanda Resource Report Resource Website 1+ mentions |
MS Amanda (RRID:SCR_018396) | software application, data analysis software, algorithm resource, software resource, data processing software | Software scoring system to identify peptides out of tandem mass spectrometry data using database of known proteins. Universal identification algorithm optimized for high resolution and high accuracy tandem mass spectra. Software tool as peptide and protein identification algorithm developed by Bioinformatics Research Group University of Applied Sciences Upper Austria in close cooperation with group of Karl Mechtler at IMP Vienna, Austria. | Tandem mass spectrometry, protein database, scoring system, peptide identification, data, search algorithm, protein identification algorithm, peptide identification, proteomic | is related to: PeptideShaker | Austrian Science Fund ; European Community Seventh Framework Programme ; MeioSys |
PMID:24909410 | Free, Available for download, Freely available | https://ms.imp.ac.at/?goto=msamanda | SCR_018396 | MS Amanda 2.0, Universal Identification Algorithm Optimized for High Accuracy Tandem Mass Spectra | 2026-07-28 09:44:56 | 2 | ||||||
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Interactive Dotplot Resource Report Resource Website 1+ mentions |
Interactive Dotplot (RRID:SCR_018329) | service resource, data access protocol, software resource, production service resource, web service, analysis service resource | Web-based tool to create customized interactive graphics, including univariate scatterplots, box plots, and violin plots, for comparing values of continuous variable across different study groups, visualization of subgroups or clusters of non-independent data. Web visualization tool for creating dot plots, box plots and violin plots for small sample size data sets. | Customized interactive graphic, univariate scatterplot, box plot, violin plot, continuous variable comparing, across different study group, subgroup visualization, subgroup cluster, non independent data visualization, data, data set | NCATS UL1 TR000135 | PMID:28974579 | Free, Freely available | SCR_018329 | 2026-07-28 09:44:54 | 1 | |||||||||
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Machado Resource Report Resource Website 1+ mentions |
Machado (RRID:SCR_018428) | application programming interface, data or information resource, data access protocol, 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 | 2026-07-28 09:44:45 | 2 | |||||||
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CohortMethod Resource Report Resource Website 10+ mentions |
CohortMethod (RRID:SCR_018511) | software application, data analysis software, software resource, data processing software, data visualization software | 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 | 2026-07-28 09:44:58 | 10 | ||||||||||
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SEDFIT Resource Report Resource Website 10+ mentions |
SEDFIT (RRID:SCR_018365) | software application, software resource, data analysis software, data processing software | Software tool for analytical ultracentrifugation developed by Dynamics of Macromolecular Assembly group of Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, NIH. Used for biophysical analysis of macromolecular assembly. | Analytical ultracentrifugation, biophysical analysis, macromolecular assembly, data, analysis, National Institute of Biomedical Imaging and Bioengineering | is listed by: SoftCite | NIH | Free, Available for download, Freely available | SCR_018365 | SEDFIT version 14.7g | 2026-07-28 09:44:44 | 25 | ||||||||
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TinderMIX Resource Report Resource Website 1+ mentions |
TinderMIX (RRID:SCR_018364) | software application, software resource, data analysis software, data processing software | Software tool as framework for dose and time dependent gene expression analysis which aims to identify groups of genes that show dynamic dose response behaviour. Software R package to cluster gene expression by contour plots. Used to analyse toxicogenomics data with multiple dose levels and time points and to identify expression patterns with respect to both variables and to cluster molecular features. | Dose dependent gene expression, time dependent gene expression, gene expression analysis, dose response, cluster gene expression, contour plot, toxicogenomics data analysis, time point, dose level, expression pattern identification, data | Free, Available for download, Freely available | https://rdrr.io/github/angy89/TinderMIX/, https://github.com/angy89/TinderMIX/ | SCR_018364 | Time-Dose INtegrated moDelling of toxicogenomics data | 2026-07-28 09:44:40 | 1 | |||||||||
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PredGPI Resource Report Resource Website 10+ mentions |
PredGPI (RRID:SCR_018363) | service resource, data or information resource, data access protocol, software resource, production service resource, web service, analysis service resource | Prediction system for GPI-anchored proteins. Used to predict presence of GPI-anchor and position of omega site. Prediction server based on support vector machine for discrimination of anchoring signal, and on Hidden Markov Model for prediction of most probable omega site. Method for screening whole proteomes. | GPI anchored protein predictor, GPI anchored protein, predict presence of GPI anchor, predict position of omega site, discrimination of anchoring signal, prediction of probable omega site, data, screening whole proteome | European Union VI Framework Programme ; FIRB 2003 LIBI–International Laboratory of Bioinformatics |
PMID:18811934 | Free, Freely available | SCR_018363 | 2026-07-28 09:44:55 | 17 | |||||||||
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STARANISO Resource Report Resource Website 50+ mentions |
STARANISO (RRID:SCR_018362) | service resource, data access protocol, software resource, production service resource, web service, analysis service resource | Web server for anisotropy of diffraction limit and Bayesian estimation of structure amplitudes by Global Phasing Limited. Server uses DEBYE and STARANISO software to perform anisotropic cut off of merged intensity data, to perform Bayesian estimation of structure amplitudes and to apply anisotropic correction to data. | Anisotropy, diffraction limit, Bayesian estimation, structure amplitude, Global Phasing Limited, anisotropic cut off, data, anisotropic correction data | Global Phasing Consortium | Free, Freely available | SCR_018362 | The STARANISO Server, STARANISO Server, STARANISO server | 2026-07-28 09:44:44 | 70 | |||||||||
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piNET Resource Report Resource Website 1+ mentions |
piNET (RRID:SCR_018693) | service resource, data access protocol, software resource, production service resource, web service, analysis service resource | 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 | NHLBI U54 HL127624; NIEHS P30 ES006096; NIMH R01 MH107487; NCI T32 CA236764; NCATS UL1 TR001425; NIGMS U01 GM120953 |
DOI:10.1093/nar/gkaa436 | Free, Freely available | SCR_018693 | 2026-07-28 09:44:48 | 4 |
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