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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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R package: LMERConvenienceFunctions Resource Report Resource Website 1+ mentions |
R package: LMERConvenienceFunctions (RRID:SCR_015658) | data processing software, data visualization software, software application, software toolkit, software resource, data analysis software | Software package that performs backward selection of fixed effects, forward fitting of the random effects, and post-hoc analysis using parallel capabilities. Other functionality includes the computation of ANOVAs with upper- or lower-bound p-values and R-squared values for each model term, model criticism plots, data trimming on model residuals, and data visualization. | r, fixed effect, random effect, anova, p-value, r-squared, data trimming, data visualization | is listed by: CRAN | Free, Available for download | SCR_015658 | LMERConvenienceFunctions, Package ‘LMERConvenienceFunctions’, LMERConvenienceFunctions: Model Selection and Post-hoc Analysis for (G)LMER Models | 2025-05-12 11:17:00 | 3 | |||||||||
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R package: lattice Resource Report Resource Website 10+ mentions |
R package: lattice (RRID:SCR_015662) | data visualization software, data processing software, software application, software resource | Data visualization software inspired by Trellis graphics, with an emphasis on multivariate data. Lattice is sufficient for typical graphics needs as well as most nonstandard requirements. | r, r package, multivariate data, data visualization | is listed by: CRAN | Free, Available for download | SCR_015662 | lattice, lattice: Trellis Graphics for R, Package ‘lattice’ | 2025-05-12 11:17:00 | 11 | |||||||||
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JIV: A 3D Image Data Visualization and Comparison Tool Resource Report Resource Website |
JIV: A 3D Image Data Visualization and Comparison Tool (RRID:SCR_008657) | 3d visualization software, data processing software, data visualization software, software resource, software application | JIV is a Java software for visualization and side-by-side comparison of multiple 3D image datasets. While it was originally designed for remote data access, it can be used as a traditional local application as well. It features include being highly portable and platform-independent, the ability to run with a common Web browser and to cope with slow network links, an independent 3D image data format, and a display of gray-level (intensity) image data with a user-controlled color-mapping, among other features. | data visualization, java, mapping, platform, software, 3D visualization | has parent organization: McGill University; Montreal; Canada | nif-0000-33046 | SCR_008657 | JIV | 2025-05-12 11:10:13 | 0 | |||||||||
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Biological Concept Diagram Editor Resource Report Resource Website |
Biological Concept Diagram Editor (RRID:SCR_008654) | BCDE | data visualization software, data processing software, software application, software resource | Biological Concept Diagram Editor (BCDE) is a conceptual relationship diagramming tool specifically designed for biomedical researchers. It allows for efficient knowledge and data capture, fast diagram creation, easy data retrieval, and flexible exporting. The BCDE application is the main diagramming tool in the system. Through it, users can create, modify, load, and save BCDE diagrams. The diagrams created with BCDE application are network oriented. Each BCDE figure can be annotated using fields from the BioPAX level II format. In addition, a user can add URL links and attachments to a BCDE figure. Diagrams generated in BCDE are stored in the BCDE XML format for better database integration and better data extraction. | biological, biomedical, concept, data visualization, diagram, drawing, research, software, tool |
is related to: National Center for Integrative Biomedical Informatics has parent organization: University of Michigan; Ann Arbor; USA |
nif-0000-33033 | SCR_008654 | 2025-05-12 11:10:13 | 0 | |||||||||
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Umap Resource Report Resource Website 100+ mentions |
Umap (RRID:SCR_018217) | UMAP | data processing software, data visualization software, software resource, software toolkit, software application | 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 | Uniform Manifold Approximation and Projection | 2025-05-12 11:19:43 | 139 | |||||||
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SnpHub Resource Report Resource Website 1+ mentions |
SnpHub (RRID:SCR_018177) | software resource, web application | Web Shiny-based server framework for retrieving, analyzing and visualizing large genomic variations data. | Genomic, data, data visualization, data analysis, data retrieving, bio.tools |
is listed by: Debian is listed by: bio.tools |
National Natural Science Foundation of China 31701415; National Key Research and Development Program of China 2018YFD0100803; National Key Research and Development Program of China 2016YFD0100801 |
Free, Available for download, Freely available | biotools:SnpHub | http://guoweilong.github.io/SnpHub/ https://bio.tools/SnpHub |
SCR_018177 | 2025-05-12 11:19:41 | 1 | |||||||
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PlotTwist Resource Report Resource Website 10+ mentions |
PlotTwist (RRID:SCR_018331) | web service, software resource, data access protocol, analysis service resource, production service resource, service resource | 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 | PlotTwist Shiny | 2025-05-12 11:19:50 | 10 | ||||||
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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 | 2025-05-12 11:19:49 | 262 | ||||||||||
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FlowPy Resource Report Resource Website 1+ mentions |
FlowPy (RRID:SCR_018195) | data processing software, data visualization software, software application, software resource, data analysis software | Software Python tool for flow cytometry data. Data generated by flow cytometer can be read by FlowPy. Used for data extraction, data visualization, data clustering, histogram subtraction. | Flow cytometry data, data extraction, data visualization, data clustering, histogram subtraction | Free, Available for download, Freely available | SCR_018195 | 2025-05-12 11:19:42 | 2 | |||||||||||
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Machado Resource Report Resource Website 1+ mentions |
Machado (RRID:SCR_018428) | web service, software resource, application programming interface, data or information resource, data access protocol | 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 | 2025-05-12 11:19:55 | 2 | |||||||
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CohortMethod Resource Report Resource Website 1+ mentions |
CohortMethod (RRID:SCR_018511) | data processing software, data visualization software, software application, software resource, data analysis 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 | 2025-05-12 11:19:59 | 9 | ||||||||||
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Repetier Host Resource Report Resource Website 10+ mentions |
Repetier Host (RRID:SCR_018901) | 3d visualization software, data processing software, data visualization software, software resource, software application | Open source 3D printing software which supports multi part printing and has slicers. | 3D printing, multi part printing support, slicer, data visualization, 3D visualization | Free, Available for download, Freely available | SCR_018901 | Repetier-Host | 2025-05-12 11:20:23 | 10 | ||||||||||
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UCSC Xena Resource Report Resource Website 1000+ mentions |
UCSC Xena (RRID:SCR_018938) | web service, software resource, portal, data or information resource, data access protocol, analysis service resource, production service resource, service resource | 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 | 2025-05-12 11:20:27 | 2097 | ||||||||
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o²S²PARC Resource Report Resource Website 1+ mentions |
o²S²PARC (RRID:SCR_018997) | osparc | software resource, software application, simulation software | 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 Project is organization facet of: SPARC Project |
Free, Freely available | SCR_018997 | open online Simulation platform for Stimulating Peripheral Activity to Relieve Conditions | 2025-05-12 11:20:33 | 1 | ||||||||
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NEMAR Resource Report Resource Website 1+ mentions |
NEMAR (RRID:SCR_019100) | topical portal, portal, data or information resource | Portal for human electrophysiological data, supports, sharing and in depth analysis of identified human neuroelectromagnetic brain data including scalp EEG, its magnetic counterpart, MEG, and, intracranial iEEG and ECoG. Open access EEG and MEG data archives, analysis, and visualization. Neuroelectromagnetic data, tools, and compute resource. | Human electrophysiological data, neuroelectromagnetic data, neuroelectromagnetic tools, data archives, data analysis, data visualization, EEG data, MEG data, iEEG data, ECoG data, brain data | is affiliated with: OpenNeuro | NIH | Free, Freely available | SCR_019100 | NEuroelectroMagnetic data Archive and tools Resource | 2025-05-12 11:20:37 | 6 | ||||||||
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CAIRN Resource Report Resource Website |
CAIRN (RRID:SCR_019101) | data processing software, web service, data visualization software, software resource, software application, data access protocol | Web tool to graph all copy number alterations present in segment file. Custom data is permitted. Allows to display copy number alterations which overlap user specified region, to quantify number of amplified CNAs and deleted CNAs. Visualization tool to explore copy number alterations discovered in published cancer datasets. Intended to help oncology community observe of relative rates of amplification, deletion, and mutation of interesting genes and regions. | Deleted CNAs quantification, Copy Number Alterations, segment file, data visualization, published cancer datasets CNAs, amplified CNA quantification | Nine Girls Ask Foundation ; NCI CA207729; NIGMS GM132055; NCI CA107263; NCI CA177519; NCI CA102310; NIA AG033082; NCI P30 CA138313 |
PMID:31923184 | Free, Available for download, Freely available | https://github.com/jrdelaney/CAIRN | SCR_019101 | Copy Alterations Intuitive Rendering Navigator | 2025-05-12 11:20:37 | 0 | |||||||
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MSstats Resource Report Resource Website 100+ mentions |
MSstats (RRID:SCR_014353) | data analysis software, data processing software, software application, software resource | A package for statistical relative quantification of proteins and peptides in global, targeted, and data-independent proteomics. It handles shotgun, label-free, and label-based Selected Reaction Monitoring, as well as SWATH/DIA (Data Independent Acquisition) experiments. MSStats provide functionality for data processing and visualization, model-based statistical analysis, and model-based sample size calculations. | data independent acquisition, statistical relative quantification, protein, peptide, data analysis software, data processing, data visualization, proteomics |
uses: R Project for Statistical Computing is used by: Skyline is listed by: Bioconductor |
National Science Foundation CAREER award 1054826 | DOI:10.1186/1471-2105-13-S16-S6 | Acknowledgement requested, Available for download | http://www.bioconductor.org/packages/release/bioc/html/MSstats.html | SCR_014353 | MSStats | 2025-05-12 11:15:31 | 173 | ||||||
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JMP Resource Report Resource Website 100+ mentions |
JMP (RRID:SCR_014242) | data processing software, data management software, data visualization software, software resource, software application | Statistical software that uses dynamic graphics rather than tables or graphs to visualize raw data. More specific versions of JMP are available for statistical analyses, clinical work, and genomics. Features include statistical modeling, data cleanup, automation and scripting, and experimental design. | statistical software, data visualization, data management, graphic data visualization |
is listed by: Metabolomics Workbench is listed by: SoftCite |
Pay for product, Free trial download is available | SCR_014242 | 2025-05-12 11:15:25 | 175 | ||||||||||
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pubatlas.org Resource Report Resource Website 1+ mentions |
pubatlas.org (RRID:SCR_014538) | data visualization software, data processing software, software application, software resource | A program that searches PubMed to generate a heat map using a user's search terms. It also allows you to see over the years how many publications there are with the user's search term(s). | atlas, pubmed, heat map, search term, data visualization | PMID:21347177 | SCR_014538 | PubAtlas: Association Explorer, PubAtlas | 2025-05-12 11:15:40 | 4 | ||||||||||
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inVUE Resource Report Resource Website 1+ mentions |
inVUE (RRID:SCR_014608) | data processing software, data visualization software, software application, software resource, data analysis software | An API and software suite for large scale data visualization and analysis. | microbiome, api, data visualization, data analysis, software | is listed by: Human Microbiome Project | SCR_014608 | 2025-05-12 11:15:45 | 1 |
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