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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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ANGSD Resource Report Resource Website 10+ mentions |
ANGSD (RRID:SCR_021865) | data analysis software, data processing software, software application, software resource | Software tool fo analysis of next generation sequencing data. Calculates various summary statistics, and performs association mapping and population genetic analyses utilizing full information in next generation sequencing data by working directly on raw sequencing data or by using genotype likelihoods. | analysing NGS data, next generation sequencing data analysis, raw sequencing data, genotype likelihoods | DOI:10.1186/s12859-014-0356-4 | Free, Available for download, Freely available | http://www.popgen.dk/angsd/index.php/ANGSD | SCR_021865 | Analysis of Next Generation Sequencing Data | 2026-09-19 12:54:59 | 47 | ||||||||
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Arthropoda Assembly Assessment Catalog Resource Report Resource Website 1+ mentions |
Arthropoda Assembly Assessment Catalog (RRID:SCR_021864) | a3cat, A3Cat | catalog, data or information resource, database | Database of metadata and assembly quality metrics for all Arthropod assemblies on NCBI. | Metadata and assembly quality metrics, Arthropod assemblies, NCBI | DOI:10.1101/2021.10.15.464561 | Free, Available for download, Freely available | https://gitlab.com/evogenlab/a3cat-workflow | SCR_021864 | Arthropoda Assembly Assessment Catalogue | 2026-09-19 12:54:59 | 2 | |||||||
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Platform for Epigenomic and Genomic Research Resource Report Resource Website 1+ mentions |
Platform for Epigenomic and Genomic Research (RRID:SCR_021861) | PEGR | data access protocol, software resource, web service | Web service platform logging metadata for genomic samples and high throughput sequencing, manages data processing workflows, and provides quality control reporting and visualization. PEGR links people, samples, protocols, sequencing and bioinformatics computation to comply with FAIR best practices for publications and data management plans.Tracks and quality controls experiments from conception to publication ready figures, compatible with multiple assays and bioinformatic pipelines. It supports rigor and reproducibility for biochemists working at wet bench, while continuing to fully support reproducibility and reliability for bioinformaticians through integration with Galaxy platform. | FAIR compliance, platform logging metadata, genomic samples, high throughput sequencing, experiments quality controls, tracking experiments, rigor and reproducibility support | DOI:10.1101/2021.07.26.453821 | Free, Available for download, Freely available | SCR_021861 | 2026-09-19 12:54:59 | 8 | |||||||||
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Phenex Resource Report Resource Website 1+ mentions |
Phenex (RRID:SCR_021748) | software resource | Software application for annotating character matrix files with ontology terms. Character states can be annotated using Entity-Quality syntax, where entity, quality, and possibly related entities are drawn from requisite ontologies. In addition, taxa (the rows of a character matrix) can be annotated with identifiers from taxonomy ontology. Phenex saves ontology annotations alongside original free text character matrix data using new NeXML format standard for evolutionary data. | phenotype, ontology, taxonomy ontology, taxa, ontology annotations, free text character matrix data, NeXML, evolutionary data | NHGRI HG002659; NSF DBI 0641025; NSF EF0423641 |
DOI:10.1371/journal.pone.0010500 | Free, Available for download, Freely available | https://github.com/phenoscape/Phenex/wiki#download--installation | SCR_021748 | 2026-09-19 12:54:57 | 1 | ||||||||
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Trialdesign Resource Report Resource Website 10+ mentions |
Trialdesign (RRID:SCR_021749) | data or information resource, portal, topical portal | Integrated platform for designing clinical trials. | Clinical trial, education, training, study design, innovative adaptive clinical trial designs | Free, Freely available | SCR_021749 | Trialdesign.org | 2026-09-19 12:54:57 | 17 | ||||||||||
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FlashPCA Resource Report Resource Website 10+ mentions Issue |
FlashPCA (RRID:SCR_021680) | data analysis software, data processing software, software application, software resource | Software tool as fast principal component analysis of large scale genome wide data. FlashPCA performs fast principal component analysis (PCA) of single nucleotide polymorphism (SNP) data. FlashPCA2 used for principal component analysis of biobank scale genotype datasets. | Principal component analysis, large scale genome wide data, single nucleotide polymorphism data, biobank scale genotype datasets | DOI:10.1093/bioinformatics/btx299 DOI:10.1371/journal.pone.0093766 |
Free, Available for download, Freely available | SCR_021680 | FlashPCA2 | 2026-09-19 12:54:56 | 38 | |||||||||
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Aquaria Resource Report Resource Website |
Aquaria (RRID:SCR_021834) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web application to help biologists use 3D structures to gain insight into protein function. Used in revealing novel insights into molecular mechanisms underlying protein function in health and disease. System for incorporating 3D structures into variant analysis. | molecular mechanisms underlying protein function, incorporating 3D structures into variant analysis | is related to: Aquaria COVID Resource | DOI:10.1101/2021.09.10.459756 | Free, Freely available | https://aquaria.app | SCR_021834 | Aquaria.App | 2026-09-19 12:54:58 | 0 | |||||||
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Aquaria COVID Resource Resource Report Resource Website |
Aquaria COVID Resource (RRID:SCR_021835) | data access protocol, software resource, web service | Web tool to visually summarise all available 3D structural information for all proteins comprising COVID-19 virus (SARS-CoV-2). Resource also gives access to structural models, generated by finding all sequence regions with detectable similarity to any currently published 3D structure. These structures are clustered into distinct states that provide insight into viral replication, mimicry, and hijacking. | 3D protein structural information, COVID-19, SARS-CoV-2, structural models | is related to: Aquaria | Free, Freely available | https://aquaria.ws/covid, https://aquaria.ws/covid#info | SCR_021835 | Aquaria-COVID Resource | 2026-09-19 12:54:58 | 0 | ||||||||
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Microns Explorer Resource Report Resource Website 10+ mentions |
Microns Explorer (RRID:SCR_021678) | data or information resource, portal, topical portal | Portal to release connectivity and functional imaging data collected by consortium of laboratories led by groups at Allen Institute for Brain Science, Princeton University, and Baylor College of Medicine, with support from broad array of teams, coordinated and funded by IARPA MICrONS program. Data include large scale electron microscopy based reconstructions of cortical circuitry from mouse visual cortex, with corresponding functional imaging data from those same neurons. | Connectome, mouse, cortex, electron microscopy, functional imaging data, cortical circuitry reconstruction, neuron |
is related to: Allen Institute for Brain Science is related to: Princeton University; New Jersey; USA is related to: Baylor College of Medicine; Houston; Texas |
IARPA MICrONS | Free, Freely available | SCR_021678 | MICrONS Explorer | 2026-09-19 12:54:56 | 19 | ||||||||
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NanoString: nCounter Analysis System Resource Report Resource Website 10+ mentions |
NanoString: nCounter Analysis System (RRID:SCR_021712) | nCounter | instrument resource | System includes hardware and software. Options include nCounter SPRINT,nCounter MAX or nCounter FLEX. Platform used for multiplex analysis of up to 800 RNA, DNA, or protein targets. System can be combined with GeoMx Digital Spatial Profiler (DSP) to enable high-plex, spatially-resolved RNA, and protein quantification. | Multiplex analysis, RNA analysis, DNA analysis, Protein analysis, NanoString Differential Expression, NanoString, analysis system, instrument, equipment, USEDit, ABRF | is listed by: USEDit | Commercially available | SCR_021712 | nCounter Analysis System, Bruker nCounter Analysis System | 2026-09-19 12:54:57 | 36 | ||||||||
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StimGen Resource Report Resource Website 1+ mentions |
StimGen (RRID:SCR_021676) | data processing software, data visualization software, software application, software resource | Software tool as interface for designing and presenting visual stimuli. | Retina, Visual Stimulation, Design, Presentation | SCR_021676 | 2026-09-19 12:54:56 | 3 | ||||||||||||
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YAML Resource Report Resource Website 10+ mentions |
YAML (RRID:SCR_021710) | software resource | YAML is a human friendly data serialization language for all programming languages. Unicode based data serialization language designed around common native data types of agile programming languages. Useful for programming needs ranging from configuration files to Internet messaging to object persistence to data auditing. | Data serialization language, common native data types, agile programming languages, configuration files, Internet messaging, object persistence, data auditing | Free, Freely available | https://yaml.org/spec/1.2.1/ | SCR_021710 | YAML 1.2 | 2026-09-19 12:54:57 | 23 | |||||||||
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TriKinetics: Drosophila Activity Monitoring System Resource Report Resource Website 10+ mentions |
TriKinetics: Drosophila Activity Monitoring System (RRID:SCR_021798) | instrument resource | System from TriKinetics for monitoring Drosophila activity. Includes hardware and DAMSystem3 Software for data acquision and DAMFileScan Software for scanning data for errors. Applied to behavioral activity experiments, including sleep deprivation analyses and general studies of hypoactivity and hyperactivity. | monitoring Drosophila activity, behavioral activity experiment, behavioral activity, activity monitoring |
is related to: TriKinetics DAMSystem3 Software is related to: Trikinetics DAM FileScan |
DOI:10.1101/pdb.prot5518 | Restricted | SCR_021798 | Drosophila Activity Monitoring System, DAM, DAM System, Drosophila Activity Monitor | 2026-09-19 12:54:58 | 13 | ||||||||
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PyCaret Resource Report Resource Website 50+ mentions |
PyCaret (RRID:SCR_021695) | software library, software resource, software toolkit | Open source, low code machine learning library in Python that allows you to go from preparing your data to deploying your model within minutes in your choice of notebook environment. | Machine learning library, Python | Free, Available for download, Freely available | https://github.com/pycaret/pycaret | SCR_021695 | PyCaret 2.3 | 2026-09-19 12:54:57 | 67 | |||||||||
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ZEN-ZEISS Efficient Navigation Resource Report Resource Website 100+ mentions |
ZEN-ZEISS Efficient Navigation (RRID:SCR_021725) | ZEN | data acquisition software, data processing software, data visualization software, image processing software, software application, software resource | Software package for ZEISS light microscopy systems. Universal user interface for every imaging system from ZEISS to assist to acquire images, process images, visualize big data by GPU powered 3D engine, analyze images via Machine Learning-based tools, correlate between light-light or light-electron microscopes, store raw data in secure format locally or in the cloud., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | ZEISS light microscopy, ZEISS, imaging | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_021725 | ZEN2010 B SP1 software, ZEISS Efficient Navigation, ZEN - ZEISS Efficient Navigation | 2026-09-19 12:54:57 | 145 | |||||||||
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MutaRNA Resource Report Resource Website 1+ mentions |
MutaRNA (RRID:SCR_021723) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web server predicts and visualizes mutation induced structure changes of single nucleotide polymorphism in RNA sequence. This covers changes in accessibility (single strandedness) of molecule, its intra molecular base pairing potential and its base pairing probabilities. One of Freiburg RNA tools. | Mutation induced structure changes, single nucleotide polymorphism, RNA sequence | has parent organization: University of Freiburg; Baden-Wurttemberg; Germany | Baden-Wuerttemberg Ministry of Science ; Research and Art ; German Research Foundation ; Germany Excellence Strategy ; University of Freiburg |
PMID:32392303 | Free, Freely available | SCR_021723 | Mutational Analysis of RNAs | 2026-09-19 12:54:57 | 2 | |||||||
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DiPer Resource Report Resource Website 1+ mentions |
DiPer (RRID:SCR_021720) | data analysis software, data processing software, software application, software resource | Software tool calculates direction autocorrelation, plots and calculates other essential parameters to analyze cell migration in two dimensions: it displays cell trajectories individually and collectively, and it calculates average speed and mean square displacements (MSDs) to assess the area explored by cells over time. | calculates direction autocorrelation, analyze cell migration, displays cell trajectories, calculates average speed and mean square displacements | SCR_021720 | 2026-09-19 12:54:57 | 3 | ||||||||||||
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NIH NCI list of FDA approved cancer drugs Resource Report Resource Website 10+ mentions |
NIH NCI list of FDA approved cancer drugs (RRID:SCR_021841) | data or information resource, disease-related portal, portal, topical portal | Portal to find consumer friendly information about drugs for cancer and conditions related to cancer. The list is in alphabetical order by generic name and brand name. | drugs for cancer, conditions related to cancer, alphabetical order, generic name, brand name | cancer | Free, Available for download, Freely available | SCR_021841 | 2026-09-19 12:54:58 | 16 | ||||||||||
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VAMPIRE Resource Report Resource Website 1+ mentions |
VAMPIRE (RRID:SCR_021721) | data analysis software, data processing software, image analysis software, software application, software resource | Software tool for analysis of cell and nuclear morphology from fluorescence or bright field images. Enables profiling and classification of cells into shape modes based on equidistant points along cell and nuclear contours. Robust method to quantify cell morphological heterogeneity. | cell morphology analysis, nuclear morphology analysis, fluorescence images, bright field images | NCI R01 CA174388; NCI U54 CA143868; NIA P30 AG021334; NIA U01 AG060903 |
DOI:10.1038/s41596-020-00432-x | Free, Available for download, Freely available | SCR_021721 | Visually Aided Morpho-Phenotyping Image Recognition | 2026-09-19 12:54:57 | 2 | ||||||||
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SARS-CoV-2 network analysis Resource Report Resource Website 1+ mentions |
SARS-CoV-2 network analysis (RRID:SCR_021811) | 1d time-series analysis software, data analysis software, data processing software, network analysis software, software application, software resource, time-series analysis software | Software tool to predict human proteins that interact with SARS-CoV-2 proteins and trace provenance of predictions. | network propagation; interpretable machine learning; provenance tracing; SARS-CoV-2; COVID-19; virus-host protein interaction networks | Free, Available for download, Freely available | SCR_021811 | SARS-CoV-2-network-analysis, SARS-CoV-2 Protein Interaction Network Analysis | 2026-09-19 12:54:58 | 1 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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