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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.
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.
Proper citation: FlowPy (RRID:SCR_018195) Copy
https://github.com/lmb-embrapa/machado
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.
Proper citation: Machado (RRID:SCR_018428) Copy
https://github.com/OHDSI/CohortMethod
Software R package for performing new user cohort studies in observational database in OMOP Common Data Model.
Proper citation: CohortMethod (RRID:SCR_018511) Copy
Open source 3D printing software which supports multi part printing and has slicers.
Proper citation: Repetier Host (RRID:SCR_018901) Copy
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.
Proper citation: UCSC Xena (RRID:SCR_018938) Copy
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.
Proper citation: o²S²PARC (RRID:SCR_018997) Copy
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.
Proper citation: NEMAR (RRID:SCR_019100) Copy
https://delaney.shinyapps.io/CAIRN/
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.
Proper citation: CAIRN (RRID:SCR_019101) Copy
https://github.com/aidenlab/Juicebox
Visualization and analysis software for Hi-C data.
Proper citation: Juicebox (RRID:SCR_021172) Copy
https://lookerstudio.google.com/
Former name Google Data Studio, is online tool for converting data into customizable informative reports and dashboards introduced by Google on March 15, 2016 as part of enterprise Google Analytics 360 suite. Online service for graphic data visualization.
Proper citation: Google Looker Studio (RRID:SCR_023549) Copy
Web based notebook that enables data driven, interactive data analytics and collaborative documents with SQL, Scala, Python, R and more. Multi purposed web based notebook which brings data ingestion, data exploration, visualization, sharing and collaboration.
Proper citation: Apache Zeppelin (RRID:SCR_023637) Copy
http://amide.sourceforge.net/index.html
Software tool for viewing, analyzing, and registering volumetric medical imaging data sets. It has been written on top of GTK+ and runs on any system that supports this toolkit (Linux, Windows, Mac OS X, etc.). The program incorporates automatic non-orthogonal data reslicing, allowing multiple data set to be fused without imposed constraints on the dimensions, anisotrophy, or voxel sizes of the data. Additional features include 3D ROI (ellipses, cylinders, boxes, and isocontours), multi-slice viewing, volume rendering, and data importing through the (X)MedCon library.
Proper citation: amide (RRID:SCR_005940) Copy
Scientific and engineering development software for numerical computations, data analysis and data visualization based on Python programming language, Qt graphical user interfaces and Spyder interactive scientific development environment. Used to interpreted languages (such as MATLAB or IDL) or compiled languages (C/C++ or Fortran) to switch to Python.
Proper citation: Pythonxy (RRID:SCR_006903) Copy
http://jsu.eagle-i.net/i/0000012b-00bc-09f9-3984-bcfb80000000
Core facility that provides the following services: Equipment access. Jackson State University Visualization Laboratory is part of the Trent Lott Geospatial and Visualization Research Center (TLGVRC). It is a research laboratory specializing in virtual reality and real-time interactive computer graphics. The mission of the visualization laboratory is to ensure highly advanced technical and theoretical visualization support to scientific research. Our goal is to provide a well-integrated and diverse scientific visualization knowledge and tools to the students, staff, and faculty.
Proper citation: JSU Visualization Laboratory (RRID:SCR_009899) Copy
http://xula.eagle-i.net/i/00000134-f6b4-e33e-77e4-a45080000000
Core facility that provides the following services: Bioassays service, Functional studies service, Gene expression service, Molecular biology service, Mass spectrometry based global scale protein profiling, 2D Gel Electrophoresis, Data analysis services. The RCMI Cell and Molecular Biology Core (CMB Core) provides focused services using cell and molecular biological techniques. It also provides access, upkeep and training on ?state of the art? equipment. Funding by the RMCI allows these services to be offered at minimal cost to users of the core. Technical services and necessary consumable supplies are provided to support cancer research projects at Xavier University. The long term goal of the Cell and Molecular Biology Core is to enhance the overall biomedical research capabilities at Xavier University.
Proper citation: XULA RCMI Cell and Molecular Biology Core (RRID:SCR_010218) Copy
https://imdevsoftware.wordpress.com/imdev/
A software application of RExcel that integrates R into Excel as an embedded additon for omics tasks and analysis. It can be used specifically for tasks concerning multivariate data visualization, exploration, and analysis. imDev has interactive modules for dimensional reduction, prediction, feature selection, analysis of correlation, and generation of networked structures, all of which provide an integrated environment for systems level analysis of multivariate data.
Proper citation: imDEV (RRID:SCR_014674) Copy
https://github.com/schwartzlab-methods/too-many-cells-interactive
Web browser-based JavaScript application for visualizing hierarchical cellular populations as interactive radial tree. Allows users to explore, filter, and manipulate hierarchical data structures through intuitive interface while also enabling batch export of high-quality custom graphics.
Proper citation: TooManyCellsInteractive (RRID:SCR_025315) Copy
Interactive web application for drug screening data analysis. It includes comprehensive quality control statistics, dose-response curve fitting, and calculation of quantitative scoring parameters such as EC50, IC50, drug sensitivity score and AUC. Used to facilitate quality control, dose-response curve fitting, and data visualization.
Proper citation: Breeze web-tool (RRID:SCR_026646) Copy
A web-based interactive computational environment where you can combine code execution, text, mathematics, plots and rich media into a single document. It offers a comprehensive library on top of which more sophisticated systems can be built. The project provides an enhanced interactive environment that includes support for data visualization and facilities for distributed and parallel computation.
Proper citation: IPython (RRID:SCR_001658) Copy
https://powerbi.microsoft.com/
Microsoft software suite of business analytics tools to analyze data and share insights. Used for business and to get answers quickly with rich dashboards available on every device.
Proper citation: PowerBi (RRID:SCR_022927) Copy
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