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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Health Data Research UK COVID-19 Initiative Resource Report Resource Website |
Health Data Research UK COVID-19 Initiative (RRID:SCR_018335) | HDRUK COVID-19 Initiative | data or information resource, data repository, disease-related portal, portal, service resource, storage service resource, topical portal | Initiative to mobilize talent and partnerships across United Kingdom to coordinate and connect national data science driven research efforts related to COVID-19 to address wider impact of COVID-19 pandemic.National Institute for Health Data Science for England, Wales, Scotland and Northern Ireland, is championing use of health data to respond to COVID-19. | Health data, COVID-19, United Kingdom, data portal, data set | is listed by: Global Initiative on Sharing All Influenza Data | COVID-19 | Free, Freely available | SCR_018335 | SciCrunch Registry | 2026-09-26 02:16:06 | 0 | ||||||||
|
SAVES Resource Report Resource Website 100+ mentions |
SAVES (RRID:SCR_018219) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web server for structure validation in homology modeling. Used to validate of obtained crude models. Structure analysis and validation server. | Structure validation, homology modeling, obtained model, analysis, validation server | has parent organization: University of California at Los Angeles; California; USA | Free, Freely available | SCR_018219 | SciCrunch Registry | SAVES v5.0, Structure Analysis and Verification Server | 2026-09-26 02:16:05 | 219 | |||||||||
|
Umap Resource Report Resource Website 100+ mentions |
Umap (RRID:SCR_018217) | UMAP | data processing software, data visualization software, software application, software resource, software toolkit | Software package as dimension reduction technique that can be used for visualization similar to t-SNE, but also for general non-linear dimension reduction. Used for dimensionality reduction for visualizing single-cell data. | Dimension reduction technique, data visualization, singel cell data | is listed by: Debian | Free, Available for download, Freely available | https://github.com/lmcinnes/umap, https://sources.debian.org/src/umap-learn/ | SCR_018217 | SciCrunch Registry | Uniform Manifold Approximation and Projection | 2026-09-26 02:16:05 | 179 | |||||||
|
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 | 2026-09-26 02:16:06 | 4 | ||||||||
|
Bustools Resource Report Resource Website 10+ mentions |
Bustools (RRID:SCR_018210) | data analysis software, data processing software, software application, software resource | Software tool for manipulating BUS files for single cell RNA-Seq datasets. Used to error correct barcodes, collapse UMIs, produce gene count or transcript compatibility count matrices, and is useful for many other tasks. | Single cell RNAseq workflow, single cell RNAseq dataset, error correct barcode, collapse UMI, produce gene count, produce transcript compatibility count matrice |
is listed by: Debian is listed by: OMICtools works with: kb_python |
DOI:10.1101/673285 | Free, Available for download, Freely available | OMICS_33004 | https://sources.debian.org/src/bustools/ | SCR_018210 | SciCrunch Registry | 2026-09-26 02:16:05 | 19 | |||||||
|
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 | 2026-09-26 02:16:06 | 12 | ||||||
|
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 | 2026-09-26 02:16:07 | 10 | |||||||||
|
medRxiv Resource Report Resource Website 100+ mentions |
medRxiv (RRID:SCR_018222) | data or information resource | Free online archive and distribution server for complete but unpublished manuscripts in the medical, clinical, and related health sciences. Preprints are preliminary reports of work that have not been certified by peer review. They should not be relied on to guide clinical practice or health related behavior and should not be reported in news media as established information. Research articles, systematic reviews and meta analyses, clinical research design protocols and data articles may be posted. | Preprint, health sciences, clinical science, medical science, research articles, posted uncertified information, data, protocol, article | Free, Freely available | SCR_018222 | SciCrunch Registry | 2026-09-26 02:16:05 | 319 | |||||||||||
|
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 | 2026-09-26 02:16:06 | 0 | |||||||||
|
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 | 2026-09-26 02:16:06 | 5 | ||||||||||
|
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 | 2026-09-26 02:16:06 | 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 | 2026-09-26 02:16:06 | 400 | ||||||||||
|
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 | 2026-09-26 02:16:06 | 4 | |||||||||||
|
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 | 2026-09-26 02:16:06 | 12 | ||||||||
|
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 | 2026-09-26 02:16:06 | 0 | ||||||||||
|
YXLON: FF35 CT Resource Report Resource Website 1+ mentions |
YXLON: FF35 CT (RRID:SCR_018208) | instrument resource | Computed tomography system designed to achieve precise inspection results for wide range of applications by YXLON. Available in single or dual tube configuration, it is perfect for very small to medium sized parts inspection in automotive, electronics, aviation, and material science industries. | Computed tomography system, instrument, equipment | Restricted | https://etek-aero.com/wp-content/uploads/2022/09/FF35-CT_Brochure_en-LR-1.pdf | SCR_018208 | SciCrunch Registry | 2026-09-26 02:16:05 | 1 | ||||||||||
|
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 | 2026-09-26 02:16:06 | 2 | |||||||||
|
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 | 2026-09-26 02:16:06 | 0 | ||||||||
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Database of Immune Cell Epigenomes Resource Report Resource Website 50+ mentions |
Database of Immune Cell Epigenomes (RRID:SCR_018259) | DICE | data access protocol, data or information resource, database, software resource, web service | Database of Immune Cell Expression, Expression quantitative trait loci (eQTLs) and Epigenomics. Collection of identified cis-eQTLs for 12,254 unique genes, which represent 61% of all protein-coding genes expressed in human cell types. Datasets to help reveal effects of disease risk associated genetic polymorphisms on specific immune cell types, providing mechanistic insights into how they might influence pathogenesis. | Data set, immune cell expression, expression quantitative trait loci, epigenomics, data, cis-eQLC, gene, protein coding gene, human cell type, genetic polymorphism disease, immune cell, pathogenesis | has parent organization: La Jolla Institute for Immunology | NCRR S10 RR027366; NIAID R24 AI108564; NIH Office of the Director S10 OD016262; William K. Bowes Jr Foundation |
PMID:30449622 | Free, Freely available | SCR_018259 | SciCrunch Registry | Database of Immune Cell Expression, Expression quantitative trait loci (eQTLs) and Epigenomics | 2026-09-26 02:16:05 | 73 | ||||||
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HingeProt Resource Report Resource Website 1+ mentions |
HingeProt (RRID:SCR_018136) | data access protocol, service resource, software resource, web service | Web server for predicting rigid protein parts and flexible hinge regions connecting them in native topology of protein chains by employing elastic network (EN) models. Automated prediction of hinges in protein structures. | Predicting protein hinges, flexible hinge region, native topology, rigid protein part, elastic network model, protein structure, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:17847101 | Free, Available for download, Freely available | biotools:hingeprot | https://bio.tools/hingeprot | SCR_018136 | SciCrunch Registry | 2026-09-26 02:16:04 | 4 |
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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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