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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.
https://ncnp-cpsy-rmap.web.app/
Software tool for visualizing research papers from computational psychiatry as two dimensional map. Shows distribution of papers along neuroscientific, psychiatric, and computational dimensions to enable anyone to find niche research and deepen their understanding of the field. Database for visualizing research papers.
Proper citation: Computational Psychiatry Research Map (RRID:SCR_018942) Copy
Software application for performing unsupervised machine learning and visualization with a focus on the clustering (separating data into groups) and dimensionality reduction (finding low dimensional structure in high dimensional data) subfields of machine learning. For visualization we provide support for both the whole dataset (e.g. a scatter plot) and points (e.g. transforming a particular point into an image). * Endlessly extensible. Every clusterer, reducer, point visualizer and dataset visualizer in Divvy is a plugin. We''ve provided a few big ones (K-means, PCA, scatter plot, &c.) and we''re hoping the community will use our plugin protocol to build many more. Each plugin defines its own UI, so your algorithm can look and behave the way that you want it to without top-down constraints. * Have lots of cores? Divvy is both task and data parallel. No longer will you be waiting for one algorithm to complete before you start another. Start as many as you want and keep using the UI. Only started one? With data parallelism we''ll still push your new MacBook Pro to 800% CPU utilization. * Part of your workflow: Export your clusterings and reductions to .csv and your visualizations to .png. Use your Matlab or R data with our Matlab/R to Divvy export tools available at http://github.com/jmlewis/divvy.
Proper citation: Divvy (RRID:SCR_006336) Copy
http://www.dnastar.com/t-seqmanpro.aspx
Software for analysis and DNA sequence assembly of Sanger data. It also provides visualizations and analysis of next-gen projects assembled by SeqMan NGen.
Proper citation: Lasergene's SeqMan Pro (RRID:SCR_000283) Copy
http://www.nitrc.org/projects/erpwavelab
A toolbox developed for multi-channel time-frequency analysis of event related activity of EEG and MEG data. It provides tools for data analysis and visualization of the most commonly used measures of time-frequency transformed event related data as well as data decomposition through non-negative matrix and multi-way (tensor) factorization. The decompositions provided can accommodate additional dimensions like subjects, conditions or repeats and as such they are perfected for group analysis. The toolbox enables tracking of phase locked activity from one channel-time-frequency instance to another as well as tools for artifact rejection in the time-frequency domain.
Proper citation: ERPwavelab (RRID:SCR_014106) Copy
A software platform which enables users to conduct genetic engineering with genomic manipulation tools (provided in the platform). Genome Compiler includes multiple DNA synthesis providers, lab facility services, and advanced bioinformatics tools and genetic repositories. Data can be imported from VectorNTI, SnapGene, ApE, Clone Manager, and others. The Gibson Assembly and Restriction Ligation methods are supported by Genome Compiler.
Proper citation: GenomeCompiler (RRID:SCR_013988) Copy
https://sourceforge.net/projects/py3dn/
A set of software tools used for morphometric analysis and visualization of the 3D structure of neurons. Py3DN works exclusively with data collected with the commercial system Neurolucida.
Proper citation: Py3DN (RRID:SCR_014511) Copy
http://scidavis.sourceforge.net/
Interactive application for data analysis and visualization in the form of plots. Its main feature is its usability and its simple graphical user interface. SciDAVis runs on GNU/Linux, Windows and MacOS X.
Proper citation: SciDAVis (RRID:SCR_014643) Copy
http://dgrapov.github.io/MetaMapR/
An open-source software program for integrating enzymatic transformations with metabolite structural similarity, mass spectral similarity and empirical associations to generate connected metabolic networks and display results using data visualization techniques.
Proper citation: MetaMapR (RRID:SCR_014685) Copy
http://www.thechiselgroup.org/jambalaya
Jambalaya is a plug-in created for Protg which uses Shrimp to visualize the knowledge bases the user has created. Protg is an ontology editor and a knowledge-base editor which allows domain experts to build knowledge-based systems by creating and modifying reusable ontologies and problem-solving methods.
Proper citation: Jambalaya (RRID:SCR_013562) Copy
https://developers.google.com/chart/
A web application which allows users to create data visualizations using JavaScript that can be embedded in a web page. Users can load some Google Chart libraries, list the data to be charted, select options to customize their chart, and create a chart object with a personally chosen id. Then, in the web page, users create a
Proper citation: Google Charts (RRID:SCR_014010) Copy
http://www.tableau.com/products/desktop
A software application which utilizes drag-and-drop to create data visualizations of various formats. Users can collaborate on and discuss data and graphs that can be created from spreadsheets, databases, and big data sources. Three versions of Tableau Desktop are available: Tableau Server, Tableau Online, and Tableau Reader.
Proper citation: Tableau Desktop (RRID:SCR_013994) Copy
DICOMscope is a free DICOM viewer which can display uncompressed, monochrome DICOM images from all modalities and which supports monitor calibration according to DICOM part 14 as well as presentation states. The application is rather a feasibility study for DICOM presentation states. DICOMscope offers a print client (DICOM Basic Grayscale Print Management) which also implements the optional Presentation LUT SOP Class.
Proper citation: DICOMscope (RRID:SCR_007344) Copy
http://www.bitplane.com/go/products/filamenttracer
A software application that automatically detects neurons (dendritic trees, axons and spines), microtubules, and other filament-like structures in 2D, 3D and 4D. Imaris FilamentTracer uses strategies that involve an optimal combination of automated analysis and operator decision. The choice of the best method is an essential element in optimizing efficiency. FilamentTracer allows the choice between four complementary tracing strategies ranging from manual to automatic and utilizes a creation wizard to easily guide the user through the creations steps. It has been specifically designed to deal with the complex problem of spine analysis over time.
Proper citation: FilamentTracer (RRID:SCR_007366) Copy
Web tool for display, annotation and management of phylogenetic trees. Accessible with any modern web browser.
Proper citation: iTOL (RRID:SCR_018174) Copy
Modeling and simulation environment for study of multi scale and multicellular systems. Users can construct and simulate models of gene regulation, signaling pathways, tissue patterning and morphogenesis and explore the effects of multiscale feedbacks between these processes. Morpheus can render 2D and 3D models using graphical user interface.
Proper citation: Morpheus (RRID:SCR_014975) Copy
https://share.streamlit.io/tantar/hack/main/GP2_data_visualization.py
Software tool for GP2 data visualization.
Proper citation: GP2 Data Visualization Tool (RRID:SCR_022187) Copy
http://www.loni.usc.edu/Software/ShapeTools
Software library that is a collection of Java classes that enable Java programmers to model, manipulate and visualize geometric shapes and associated data values. It simplifies the creation of application programs by providing a ready-made set of support routines. * File format readers that implement ShapeIO interface (modeled after Java ImageIO) are automatically used when appropriate. * Storage of additional metadata of arbitrary type (other than shape vertices and interconnections) is enabled by the use of data attributes. * Shapes may contain a set of child shapes allowing for the construction and manipulation of complex hierarchies of shapes. * The various components of a shape are specified as interfaces with specific implementations, making it easy to create specialized implementations of a shape component when different performance characteristics are required.
Proper citation: LONI ShapeTools (RRID:SCR_002697) Copy
https://www.proteinspire.org/MOPED/
An expanding multi-omics resource that enables rapid browsing of gene and protein expression information from publicly available studies on humans and model organisms. MOPED also serves the greater research community by enabling users to visualize their own expression data, compare it with existing studies, and share it with others via private accounts. MOPED uniquely provides gene and protein level expression data, meta-analysis capabilities and quantitative data from standardized analysis utilizing SPIRE (Systematic Protein Investigative Research Environment). Data can be queried for specific genes and proteins; browsed based on organism, tissue, localization and condition; and sorted by false discovery rate and expression. MOPED links to various gene, protein, and pathway databases, including GeneCards, Entrez, UniProt, KEGG and Reactome. The current version of MOPED (MOPED 2.5) The current version of MOPED (MOPED 2.5, 2014) contains approximately 5 million total records including ~260 experiments and ~390 conditions.
Proper citation: MOPED - Model Organism Protein Expression Database (RRID:SCR_006065) Copy
https://github.com/galaxyproteomics/mvpapplication-git.git
Software tool as plugin to enable viewing of results produced from workflows integrating genomic sequencing data and mass spectrometry proteomics data. Plugin to Galaxy bioinformatics workbench which enables visualization of mass spectrometry-based proteomics data integrated with genomic and/or transcriptomic sequencing data. Useful for verifying quality of results and characterizing novel peptide sequences identified using multi-omic proteogenomic approach.
Proper citation: Multi-omics Visualization Platform (RRID:SCR_018077) Copy
https://huygens.science.uva.nl/PlotsOfData/
Web app for visualizing data together with their summaries. Visualizes data and statistics to enable comparison of experimental conditions. Written in R and uses packages including shiny, ggplot2, dplyr, tidyr, readr, magrittr, ggbeeswarm, readxl, DT. Github page of PlotsOfData can be used to trace changes between different versions.
Proper citation: PlotsOfData (RRID:SCR_018333) Copy
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