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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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University of Leon, Spain Resource Report Resource Website |
University of Leon, Spain (RRID:SCR_019071) | data or information resource, portal, topical portal | Spanish public university with campus in Leon and Ponferrada. | is parent organization of: Scayle | SCR_019071 | 2026-09-05 06:28:46 | 0 | ||||||||||||
|
RAPIDO Resource Report Resource Website 1+ mentions |
RAPIDO (RRID:SCR_018935) | alignment software, data access protocol, data processing software, image analysis software, software application, software resource, web service | Web server for alignment of protein structures in presence of conformational changes. Used for 3D alignment of crystal structures of different protein molecules in presence of conformational change. Can identify structurally equivalent regions also when distant in terms of sequence and separated by other movable domains. | Protein structure alignment, rapid alignment, protein domain, conformational changes presence, 3D alignment, crystal structure, protein molecule, conformational change presence, identify structural region, distant sequence, movable domains | Associazione Italiana per la Ricerca sul Cancro ; European Molecular Biology Laboratory |
PMID:18460546 PMID:18727838 |
Free, Freely available | SCR_018935 | Rapid Alignment of Proteins in terms of Domains, Rapid alignment of proteins in terms of domains | 2026-09-05 06:28:44 | 2 | ||||||||
|
UCSC Xena Resource Report Resource Website 1000+ mentions |
UCSC Xena (RRID:SCR_018938) | analysis service resource, data access protocol, data or information resource, portal, production service resource, service resource, software resource, web service | Web tool where one component is front end Xena Browser and another component is back end Xena Hubs. Web based Xena Browser empowers biologists to explore data across multiple Xena Hubs with variety of visualizations and analyses. Xena Hubs host genomics data from laptops, public servers, behind firewall, or in cloud, and can be public or private. Xena Browser receives data simultaneously from multiple Xena Hubs and integrates them into single coherent visualization within browser. Allows users to explore functional genomic data sets for correlations between genomic and/or phenotypic variables. | Data visualization, data analysis, genomics data, explore functional genomic data, functional genomic, data sets, genomic variable correlation, phenotypic variables correlation | has parent organization: University of California at Santa Cruz; California; USA | Free, Freely available | https://xenabrowser.net/ | SCR_018938 | UCSC Xena Browser, Xena Browser | 2026-09-05 06:28:44 | 4804 | ||||||||
|
o²S²PARC Resource Report Resource Website 1+ mentions |
o²S²PARC (RRID:SCR_018997) | osparc | simulation software, software application, software resource | Simulation platform that enables users to create, access, tune, and run models or computational algorithms through web based interface. Web interactive simulation platform that hosts SPARC computational models and solvers. Allows collaborative development and sharing, model coupling and cloud based execution, data visualization and analysis, and ensures sustainability of computational models developed within SPARC. Enables users to create predictive, multiscale, multi-physics models spanning from modulation sources acting on peripheral nervous system (PNS) to resulting modulation of organ functional response. | SPARC, SPARC computational model, data sharing, model coupling, cloud based execution, data visualization, data analysis, peripheral nervous system, organ functional response |
is used by: SPARC Portal is organization facet of: SPARC Portal |
Free, Freely available | SCR_018997 | open online Simulation platform for Stimulating Peripheral Activity to Relieve Conditions | 2026-09-05 06:28:45 | 2 | ||||||||
|
Protein.Plus Resource Report Resource Website 50+ mentions |
Protein.Plus (RRID:SCR_019044) | data access protocol, software resource, web service | Web server is focused on protein ligand interactions. Provides support for initial steps when dealing with protein structures, namely structure search, quality assessment, and preprocessing. Furthermore, advanced options, such as protein pocket detection, ensemble generation or prediction of metal coordinations are supported. | Protein ligand interaction, protein structure, quality assessment, protein pocket detection, ensemble generation, metal coordinations prediction | has parent organization: University of Hamburg; Hamburg; Germany | Free, Freely available | SCR_019044 | 2026-09-05 06:28:45 | 59 | ||||||||||
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fracridge Resource Report Resource Website 1+ mentions |
fracridge (RRID:SCR_019045) | 1d time-series analysis software, data analysis software, data processing software, software application, software resource, 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 | 2026-09-05 06:28:45 | 1 | |||||||
|
RAVE Resource Report Resource Website 1+ mentions |
RAVE (RRID:SCR_019040) | data analysis software, data processing software, data visualization software, software application, software resource | Open source software tool for reproducible analysis and visualization of intracranial EEG data. Used for analysis of intracranial electroencephalogram data, including data collected using strips and grids (electrocorticography, ECoG) and depth electrodes (stereotactic EEG). | Intracranial EEG data, data analysis, intracranial electroencephalogram data, electrocorticography data, depth electrodes, stereotactic EEG, iEEG data | NIMH R24 MH117529 | DOI:10.1016/j.neuroimage.2020.117341 | Free, Available for download, Freely available | SCR_019040 | R Analysis and Visualization of intracranial EEG | 2026-09-05 06:28:45 | 3 | ||||||||
|
Cello2Go Resource Report Resource Website 50+ mentions |
Cello2Go (RRID:SCR_019042) | data access protocol, software resource, web service | Web server for protein subcellular localization prediction with functional gene ontology annotation. Web based system for screening various properties of targeted protein and its subcellular localization. | Protein subcellular localization, localization prediction, functional gene ontology annotation, targeted protein properties screening |
uses: NCBI BLAST uses: CELLO works with: UniProtKB |
China Medical University of Taiwan ; National Chiao Tung University and Ministry of Education of Taiwan ; National Science Council of Taiwan |
PMID:24911789 | Free, Freely available | SCR_019042 | subCELlular LOcalization prediction with functional Gene Ontology annotation | 2026-09-05 06:28:45 | 79 | |||||||
|
PROCHECK Resource Report Resource Website 100+ mentions |
PROCHECK (RRID:SCR_019043) | data analysis software, data processing software, software application, software resource | Software tool to check stereochemical quality of protein structures. Its outputs comprise number of plots in PostScript format and comprehensive residue by residue listing. Includes PROCHECK-NMR for checking quality of structures solved by NMR. | Stereochemical quality, protein structure, plot, residue listing, protein, assessing protein quality, | is listed by: SoftCite | DOI:10.1107/S0021889892009944 | Free, Available for download | SCR_019043 | 2026-09-05 06:28:45 | 122 | |||||||||
|
scTHI Resource Report Resource Website 1+ mentions |
scTHI (RRID:SCR_018918) | scTHI | data analysis software, data processing software, software application, software resource | Software R package to identify active pairs of ligand receptors from single cells in order to study,among others, tumor host interactions. Contains set of signatures to classify cells from tumor microenvironment. | Ligand receptor, active pair, active pair ligand receptor, single cell, tumor interaction, tumor microenvironment, cells clasification | is listed by: Bioconductor | Free, Available for download, Freely available | SCR_018918 | 2026-09-05 06:28:44 | 1 | |||||||||
|
Leica: ASP300S Fully Enclosed Tissue Processor Resource Report Resource Website 1+ mentions |
Leica: ASP300S Fully Enclosed Tissue Processor (RRID:SCR_018916) | instrument resource | Processor that automatically washes tissue sample which needs to be usable in downstream processes. Designed for routine and research histopathology of up to 300 cassettes. | Leica ASP300S, tissue processor, tissue automatic wash, routine research histopathology, instrument, equipment | is listed by: USEDit | Restricted | https://www.leicabiosystems.com/sites/default/files/media_product-download/2021-03/95.11569_Brochure_ASP300_S_EN.pdf | SCR_018916 | 2026-09-05 06:28:44 | 2 | |||||||||
|
Mcule Resource Report Resource Website 10+ mentions |
Mcule (RRID:SCR_018921) | data access protocol, data or information resource, portal, software resource, web service | Software drug discovery platform to integrate purchasable chemical space with molecular modeling tools. Chemical marketplace for drug discovery with services based around small molecule compound sourcing. Integrated molecular modeling tools, compound database, IT infrastructure and compound procurement service with web interface. Virtual screens can be run to identify new hits and modeling applications can be used to improve their affinity and other properties. | Drug discovery platform, molecular modeling, molecular modeling tools, compound database, IT infrastructure, compound procurement service, web interface, virtual screening, modeling application | Restricted | SCR_018921 | 2026-09-05 06:28:44 | 46 | |||||||||||
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Hetindel Resource Report Resource Website 1+ mentions |
Hetindel (RRID:SCR_018922) | data analysis software, data processing software, software application, software resource | Software package to identify genomic insertions or deletions, so called indels, in heterozygous sequencing data where both alleles carry mutations. Used to analyze heterozygous indels. | Genomic insertions identification, genomic deletions identification, indel, heterozygous sequencing data, alleles, mutation, heterozygous indel, data | has parent organization: Max Planck Institute for Developmental Biology; Tubingen; Germany | Free, Available for download, Freely available | SCR_018922 | 2026-09-05 06:28:44 | 1 | ||||||||||
|
Progenesis QI Resource Report Resource Website 1000+ mentions |
Progenesis QI (RRID:SCR_018923) | data analysis software, data processing software, software application, software resource | Software tool as next generation in LC-MS proteomics data analysis software by Nonlinear Dynamics. | Next generation, LC-MS proteomics data, data analysis, Nonlinear Dynamics | SCR_018923 | 2026-09-05 06:28:44 | 1011 | ||||||||||||
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Urinary Stone Disease Research Network Resource Report Resource Website |
Urinary Stone Disease Research Network (RRID:SCR_019059) | USDRN | data or information resource, disease-related portal, portal, topical portal | Portal for research on urinary stones in adults and children in order to learn more about who forms kidney stones, treatments and prevention. Network comprises of experts including adult and pediatric urologists, adult and pediatric nephrologists, pediatricians, emergency department physicians, clinical trialists, nutritionists, behavioral scientists, and radiologists. Duke Clinical Research Institute is Scientific Data Research Center and with clinical sites including University of Pennsylvania Children Hospital of Philadelfia, University of Texas Southwestern Medical Center, University of Washington, Washington University in St. Louis, work together in planning, executing, and analyzing results from USDRN studies. | Urinary stone, kidney stone, kidney, treatment, prevention, urologist, nephrologist, pediatrician, clinical trial, data |
is related to: Duke University School of Medicine; North Carolina; USA is related to: University of Pennsylvania; Philadelphia; USA is related to: University of Texas System; Texas; USA is related to: Washington University in St. Louis; Missouri; USA is related to: University of Washington; Seattle; USA |
Kidney stones | NIDDK ; NIH |
Free, Freely available | SCR_019059 | 2026-09-05 06:28:46 | 0 | |||||||
|
Engauge Digitizer Resource Report Resource Website 50+ mentions |
Engauge Digitizer (RRID:SCR_019056) | data processing software, image processing software, software application, software resource | Software tool accepts image files (like PNG, JPEG and TIFF) containing graphs, and recovers the data points from those graphs. Used to convert graphs to data points. Imports image file and then digitizes it by placing points along axes and curves. | Image file acceptance, graph image, graph data recovery, graph conversion, data point, image file import, image digitization | Free, Available for download, Freely available | https://github.com/markummitchell/engauge-digitizer/tree/v12.2.1 | SCR_019056 | 2026-09-05 06:28:45 | 64 | ||||||||||
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CueMol Resource Report Resource Website 10+ mentions |
CueMol (RRID:SCR_019052) | data processing software, data visualization software, software application, software resource | Software tool for macromolecular structure visualization. Molecular visualization framework to visualize crystallographic models of macromolecules. Used to visualize and create publication quality images of macromolecular structures with user friendly interfaces. | Macromolecular structure visualization, macromolecural crystallographic model visualization, molecular structure, molecular structure image, structure image | Free, Available for download, Freely available | https://github.com/CueMol/cuemol2, https://sourceforge.net/projects/cuemol/ | SCR_019052 | Que | 2026-09-05 06:28:45 | 23 | |||||||||
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Differential Methylation Analysis Package Resource Report Resource Website |
Differential Methylation Analysis Package (RRID:SCR_019148) | DMAP | data analysis software, data processing software, software application, software resource, software toolkit | Software package for large scale genomic DNA methylation analysis. Filters and processes aligned bisulphite sequenced data to generate comprehensive reference methylomes in different units for any genome. Processes aligned SAM files of multiple samples to provide reliable and statistically significant differentially methylated regions, then relate them to proximal genes and CpG features with reasonable rapidity. | Genomic DNA methylation, DNA methylation analysis, bisulphite sequenced data, reference methylomes generation, genome, aligned SAM files processing, differentially methylated regions | has parent organization: University of Otago; Dunedin; New Zealand | National Centre for Growth and Development and Health Research Council ; New Zealand |
PMID:24608764 | Free, Freely available | SCR_019148 | 2026-09-05 06:28:46 | 0 | |||||||
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FASTQuick Resource Report Resource Website 1+ mentions |
FASTQuick (RRID:SCR_019269) | data analysis software, data processing software, software application, software resource | Software tool for rapid and comprehensive quality assessment of raw sequence reads. It generates comprehensive list of QC statistics, including ancestry and contamination estimation. | Sequenced genomes quality assessment, raw sequence reads, quality assessment, NGS sequencing fastq files, quality control, | DOI:10.1101/2020.06.10.143768 | Free, Available for download, Freely available | SCR_019269 | 2026-09-05 06:28:48 | 1 | ||||||||||
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Nurses Health Study Resource Report Resource Website 1+ mentions |
Nurses Health Study (RRID:SCR_019144) | data or information resource, portal, topical portal | Portal about prospective investigations into risk factors for major chronic diseases in women. Nurses were selected as study population because of their knowledge about health and their ability to provide complete and accurate information regarding various diseases, due to their nursing education.The largest longitudinal study of women. Started in 1976, involving 275000 participants. | Health Data and Tools | NHS | Free, Freely available | SCR_019144 | Nurses study | 2026-09-05 06:28:46 | 6 |
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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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