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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Provisional Cell Ontology Resource Report Resource Website 1+ mentions |
Provisional Cell Ontology (RRID:SCR_018332) | PCL | controlled vocabulary, data or information resource, ontology, portal | Collection of ontology of provisional cells determined by experimental methods. | Ontology, provisional cell, experimental method, BioPortal |
is related to: BioPortal is related to: BioPortal Metadata Ontology |
Free, Freely available | SCR_018332 | SciCrunch Registry | Provisional Cell Ontology | 2026-10-24 12:47:56 | 4 | ||||||||
|
PlotTwist Resource Report Resource Website 10+ mentions |
PlotTwist (RRID:SCR_018331) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web application for plotting and annotating continuous data. Open source web app for plotting and annotating time series data. Used to inspect data and generate publication quality visualizations. Available options for plotting include lineplot, small multiples and heatmap, summary statistics and inferential statistics. | Plotting continuous data, annotating continuous data, data visualization, time series data, line plot, small multiples, heatmap, statistic, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:31929523 | Free, Freely available | biotools:Plottwist, BioTools:PlotTwist | https://github.com/JoachimGoedhart/PlotTwist, https://bio.tools/PlotTwist, https://bio.tools/PlotTwist, https://bio.tools/PlotTwist | SCR_018331 | SciCrunch Registry | PlotTwist Shiny | 2026-10-24 12:47:56 | 12 | ||||||
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CRISPRcasIdentifier Resource Report Resource Website 1+ mentions |
CRISPRcasIdentifier (RRID:SCR_018296) | data analysis software, data processing software, software application, software resource | Software tool providing machine learning approach for identification and classification of CRISPR-Cas systems. Combines regression and classification approaches for improving quality of input protein cassettes and predicting their subtypes. | CRISPR-Cas, Machine Learning, Cas genes, Cas proteins, input protein cassette, predicting subtype, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1101/817619 | Free, Available for download, Freely available | biotools:crisprcasidentifier | https://bio.tools/crisprcasidentifier | SCR_018296 | SciCrunch Registry | 2026-10-24 12:47:55 | 5 | |||||||
|
Whippet Resource Report Resource Website 10+ mentions |
Whippet (RRID:SCR_018349) | data analysis software, data processing software, software application, software resource | Software tool for analysis of Alternative Splicing events and calculation of weighted transcripts per million values TPM on gene level. RNA-seq analysis method that quantifies AS events of any complexity without loss of accuracy. Used for accurate profiling AS to find misregulation present in human diseases. | Alternative Splicing analysis, alternative splicing, weighted transcripts values, TPM calculation, gene level, RNA-seq analysis, AS event quantification | Canada First Excellence Fund ; Canadian Institutes of Health Research ; EMBO Long-Term Fellowship ; Marie Curie IOF Fellowship |
PMID:30220560 | Free, Available for download, Freely available | SCR_018349 | SciCrunch Registry | 2026-10-24 12:47:56 | 10 | |||||||||
|
CORD-19 Explorer Resource Report Resource Website |
CORD-19 Explorer (RRID:SCR_018341) | data access protocol, data or information resource, disease-related portal, portal, service resource, software resource, topical portal, web service | Software tool as full text search engine for COVID-19 Open Research Dataset. Used to explore dataset and identify potential research efforts. | Full text engine, COVID-19 dataset, explore dataset, COVID-19 Open Research, dataset |
has parent organization: Allen Institute works with: COVID-19 Open Research Dataset |
COVID-19 | Free, Freely available | SCR_018341 | SciCrunch Registry | 2026-10-24 12:47:56 | 0 | |||||||||
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Crowdfight COVID-19 Resource Report Resource Website 1+ mentions |
Crowdfight COVID-19 (RRID:SCR_018340) | data or information resource, disease-related portal, portal, topical portal | Initiative from scientific community to put all available resources including highly skilled scientists at service of fight against COVID-19. | COVID-19, COVID-19 researcher, volunteer service, | COVID-19 | Free, Freely available | SCR_018340 | SciCrunch Registry | 2026-10-24 12:47:56 | 5 | ||||||||||
|
FoldIndex Resource Report Resource Website 1+ mentions |
FoldIndex (RRID:SCR_018390) | data access protocol, service resource, software resource, web service | Web tool to predict whether given protein sequence is intrinsically unfolded. Algorithm for predicting ordered and disordered regions in protein based on its primary structure amino acid sequence. Graphic web server to predict if given protein sequence is intrinsically unfolded implementing algorithm of Uversky and co-workers, which is based on average residue hydrophobicity and net charge of sequence. | Protein sequence, intrinsically unfolded sequence, protein ordered region, protein disordered region, amino acid structure, protein region prediction | Divadol Foundation ; Israel Ministry of Science and Technology ; Minerva Foundation |
DOI:10.1093/bioinformatics/bti537 | Free, Freely available | SCR_018390 | SciCrunch Registry | 2026-10-24 12:47:56 | 4 | |||||||||
|
Measurement Control And Data Analysis Software Resource Report Resource Website 1+ mentions |
Measurement Control And Data Analysis Software (RRID:SCR_018309) | MES | data analysis software, data processing software, software application, software resource | Software package for measurement control and analysis by Femtonics Ltd. Designed in MATLAB and used in field of cellular and network imaging. New version offers new scanning features and improved overall usability. | Measurement control, measurement analysis, Femtonics Ltd, cellular imaging, networking imaging, data scanning | uses: MATLAB | Restricted | SCR_018309 | SciCrunch Registry | 2026-10-24 12:47:55 | 6 | |||||||||
|
Jupyter Notebook Resource Report Resource Website 100+ mentions |
Jupyter Notebook (RRID:SCR_018315) | software resource, web application | Open source web application to create and share documents that contain live code, equations, visualizations and narrative text. Used for data cleaning and transformation, numerical simulation, statistical modeling, data visualization, machine learning. | Create and share document, live code, equation, visualization, narrative text document, data cleaning, data transformation, numerical simulation, statistical modeling, data visualization, machine learning |
is used by: NWB Explorer is related to: Jupyter-client is related to: MERMAID is related to: Docker based GPU enabled Jupyterlab is related to: JupyterLab |
Free, Available for download, Freely available | SCR_018315 | SciCrunch Registry | 2026-10-24 12:47:55 | 400 | ||||||||||
|
O Resource Report Resource Website 1+ mentions |
O (RRID:SCR_018394) | 3d spatial image, 3d visualization software, data or information resource, data processing software, data visualization software, image, software application, software resource | Software for visualization of macromolecular structures, atomic coordinates, and 3D intensity maps, and for building macromolecular structures. | Macromolecular structure, atomic coordinate, protein structure, 3D visualization, model building, atomic modelling | has parent organization: Uppsala University; Uppsala; Sweden | DOI:10.1107/s0108767390010224 | Free, Available for download, Freely available | SCR_018394 | SciCrunch Registry | 2026-10-24 12:47:56 | 1 | |||||||||
|
COVID-19 research data on Figshare Resource Report Resource Website |
COVID-19 research data on Figshare (RRID:SCR_018277) | data or information resource, portal, topical portal | Portal to discover COVID-19 open research data on Figshare. Figshare collection of COVID-19 related research data. | COVID-19, COVID-19 data, open research data | is listed by: Data and Computational Resources to Address COVID-19 | COVID-19 | Free, Freely available | SCR_018277 | SciCrunch Registry | 2026-10-24 12:47:55 | 0 | |||||||||
|
SPCM Resource Report Resource Website 1+ mentions |
SPCM (RRID:SCR_018310) | data acquisition software, data processing software, software application, software resource | Software tool as instrument software for SPC- and DPC Modules by Becker and Hickl GmbH. | Data acquisition, instrument software, Becker and Hickl GmbH | Restricted | SCR_018310 | SciCrunch Registry | 2026-10-24 12:47:55 | 4 | |||||||||||
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MS Amanda Resource Report Resource Website 1+ mentions |
MS Amanda (RRID:SCR_018396) | algorithm resource, data analysis software, data processing software, software application, software resource | 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 | SciCrunch Registry | MS Amanda 2.0, Universal Identification Algorithm Optimized for High Accuracy Tandem Mass Spectra | 2026-10-24 12:47:57 | 2 | ||||||
|
ATCOR: SphygmoCor Resource Report Resource Website 10+ mentions |
ATCOR: SphygmoCor (RRID:SCR_018323) | instrument resource | System for measuring pulse wave velocity, pulse wave analysis by ATCOR. System for noninvasive central blood pressure waveform assessment. Provides measures of central arterial pressure waveform and pulse wave velocity as well as assessment of arterial stiffness via waveform analysis e.g. augmentation index, augmented pressure, and reflected wave magnitude. | Measuring pulse, wave velocity, wave analysis, ATCOR, noninvasive blood pressure assessment, arterial stiffness, augmentation index, augmented pressure, wave magnitude | Restricted | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_018323.pdf | https://atcormedical.com/wp-content/uploads/simple-file-list/Downloads/SphygmoCor-XCEL-V1_3-Operators-Manual.pdf | SCR_018323 | SciCrunch Registry | SphygmoCor XCEL | 2026-10-24 12:47:56 | 12 | ||||||||
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Itamar: EndoPat Resource Report Resource Website |
Itamar: EndoPat (RRID:SCR_018322) | instrument resource | System for non-invasive vascular function assessment by Itamar Medical Ltd. | Non invasive test, vascular function, endothelial dysfunction diagnosis, endothelial damage measurement, Itamar Medical Ltd | Restricted | https://www.itamar-medical.com/wp-content/uploads/2019/07/OM1695214.pdf | SCR_018322 | SciCrunch Registry | 2026-10-24 12:47:56 | 0 | ||||||||||
|
Interactive Dotplot Resource Report Resource Website 1+ mentions |
Interactive Dotplot (RRID:SCR_018329) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | 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 | SciCrunch Registry | 2026-10-24 12:47:56 | 2 | |||||||||
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Jittered Boxplots for Toxicological Data Resource Report Resource Website |
Jittered Boxplots for Toxicological Data (RRID:SCR_018326) | ToxBox | data access protocol, service resource, software resource, web service | Web tool for creating box plots with dot plots. Boxplot for grouped and clustered data in toxicology. Jittered boxplots for visualizing grouped and clustered data from toxicological studies together with individual raw values and indications of statistical significance. | Box plot, dot plot, grouped data, clustered data, toxicology, visualizing data, toxicological study data, raw value, statistical significance | PMID:26438403 | Free, Freely available | SCR_018326 | SciCrunch Registry | Jittered boxplots | 2026-10-24 12:47:56 | 0 | ||||||||
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outbreak.info Resource Report Resource Website 100+ mentions |
outbreak.info (RRID:SCR_018282) | data or information resource, portal, topical portal | Resource to aggregate all outbreak information into single location during outbreaks of emerging diseases, such as COVID-19. | COVID-19 data collection, single location, outbreak information, emerging disease |
is listed by: Data and Computational Resources to Address COVID-19 has parent organization: Scripps Research Institute |
COVID-19 | NIAID | Free, Freely available | SCR_018282 | SciCrunch Registry | 2026-10-24 12:47:55 | 155 | ||||||||
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Data-Against-COVID Team Resource Report Resource Website |
Data-Against-COVID Team (RRID:SCR_018288) | data or information resource, portal, topical portal | Group of volunteer data scientists, machines learning experts, bioinformaticians and professional software developers who have joined together to offer their expertise for any data analysis problems that arise in context of ongoing coronavirus pandemic. | Data scientist, volunteer, machine learning expert, bioinformaticians, professional software developer, data analysis, coronavirus pandemic | is listed by: Data and Computational Resources to Address COVID-19 | COVID-19 | Free, Freely available | SCR_018288 | SciCrunch Registry | 2026-10-24 12:47:55 | 0 | |||||||||
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Cloud resources for COVID-19 research Resource Report Resource Website |
Cloud resources for COVID-19 research (RRID:SCR_018286) | data or information resource, portal, topical portal | Cloud resources for COVID-19 research provided by Rescale, Google Cloud, and Microsoft Azure. High performance computing resources immediately available for COVID-19 research. | Cloud resorce, COVID-19, Rescale, Google Cloud, Microsoft Azure, computing resource | is listed by: Data and Computational Resources to Address COVID-19 | COVID-19 | Free, Freely available | SCR_018286 | SciCrunch Registry | 2026-10-24 12:47:55 | 0 |
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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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