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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Computational Psychiatry Research Map Resource Report Resource Website 1+ mentions |
Computational Psychiatry Research Map (RRID:SCR_018942) | CPSYMAP | data or information resource, database | 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. | Visualizing research papers, computational psychiatry, 2D map, papers distribution, database, data visualization, paper, psychiatry | DOI:10.1101/2020.06.30.181198v1 | Free, Freely available | SCR_018942 | Computational Psychiatry Research Map Database, CPSYMAP database | 2025-05-06 11:14:08 | 1 | ||||||||
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Google Charts Resource Report Resource Website 10+ mentions |
Google Charts (RRID:SCR_014010) | software resource, web application |
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 with that id to display the Google Chart. Charts are customizable and interactive, and since they are rendered using HTML5/SVG technology, charts are cross-browser compatibility and cross platform portability to iPhones, iPads and Android.
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web application, data visualization, chart, interactive |
is listed by: Connected Researchers is related to: Connected Researchers |
Free, Public | SCR_014010 | 2025-05-12 11:15:13 | 27 | ||||||||||
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sjplot Resource Report Resource Website 50+ mentions |
sjplot (RRID:SCR_024307) | software resource, software toolkit | Software R package as collection of plotting and table output functions for data visualization. Results of various statistical analyses that are commonly used in social sciences can be visualized using this package, including simple and cross tabulated frequencies, histograms, box plots, generalized linear models, mixed effects models, principal component analysis and correlation matrices, cluster analyses, scatter plots, stacked scales, effects plots of regression models including interaction terms. This package supports labelled data. | data visualization, simple and cross tabulated frequencies, histograms, box plots, generalized linear models, mixed effects models, principal component analysis and correlation matrices, cluster analyses, scatter plots, stacked scales, effects plots of regression models including interaction terms, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-sjplot/ | SCR_024307 | 2025-05-12 11:24:56 | 78 | |||||||||
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STRAP Resource Report Resource Website 100+ mentions |
STRAP (RRID:SCR_005675) | STRAP | software resource, software application, data processing software | Software program that automatically annotates a protein list with information that helps in the meaningful interpretation of data from mass spectrometry and other techniques. It takes protein lists as input, in the form of plain text files, protXML files (usually from the TPP), or Dat files from MASCOT search results. From this, it generates protein annotation tables, and a variety of GO charts to aid individual and differential analysis of proteomics data. It downloads information from mainly the Uniprot and EBI QuickGO databases. STRAP requires Windows XP or higher with at least version 3.5 of the Microsoft .NET Framework installed. Platform: Windows compatible | protein, gene, annotation, mass spectrometry, proteomics, visualization, browser, differential analysis, analysis, ontology or annotation browser, ontology or annotation visualization, differential analysis of proteomics data sets, windows, protein annotation, data visualization, c#, pathway, FASEB list |
is listed by: Gene Ontology Tools is listed by: OMICtools is related to: Gene Ontology is related to: UniProt is related to: QuickGO has parent organization: Boston University School of Medicine; Massachusetts; USA |
NHLBI contract N01 HV28178; NCRR P41 RR10888 |
PMID:19839595 | Open unspecified license, Acknowledgement requested | OMICS_02277, nlx_149115 | SCR_005675 | Software Tool for Rapid Annotation of Proteins, STRAP for GO Annotation, STRAP - Software Tool for Rapid Annotation of Proteins | 2025-05-12 11:07:34 | 114 | |||||
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FMRLAB Resource Report Resource Website 1+ mentions |
FMRLAB (RRID:SCR_005164) | FMRLAB | software resource, software application, data processing software | A Matlab toolbox for fMRI data analysis using Independent Component Analysis (ICA). It provides an integrated environment to manage, process and analyze fMRI data in a single framework so that users can complete the analysis without switching between software. In addition, it provides an interactive Matlab graphic user interface (GUI). All the necessary processes to apply ICA to fMRI data and review its results can be run from the graphic interface. The FMRLAB processing flow is straightforward. Custom analyses can be performed with Matlab scripts using the FMRLAB functions and data structure. Since fMRI data analysis is a complex enterprise, including digital image processing, statistical analysis and data visualization, an integrated framework combining processing elements is desired eagerly by users in the neuroimaging community. Recently, large number of software tools for data analysis and visualization have been developed for this purpose. However, most of these tools use model-based statistical methods which assume that the users know the hemodynamic response (HR) for their paradigm in advance and can specify a reasonable HR model. Often, however, accurate or reasonable response HR models are unavailable. An alternative data-driven method, infomax ICA (McKeown et al., 1998), does not require that an a priori HR model, instead deriving HRs of spatially independent components of the entire data set from the higher-order statistics of the data themselves. FMRLAB is a toolbox running under Matlab containing necessary components for data-driven fMRI data analysis using the highly reliable infomax ICA algorithm (Bell & Sejnowski, 1995), normalized (Amari, 1999), extended (Lee, Girolami and Sejnowski, 1999) and automated by Makeig et al. FMRLAB has been developed under Matlab 6.1 running on Red Hat Linux. FMRLAB Features * Graphic user interface * Flexible data importing * Interactive data plotting * Computationally efficient * Defined FMRI data structure * Independent component browser * Smooth, transparent component exporting and spatial normalization process * Interface with other software for further analysis or visualization. * SPM-style component plots (MIP, 2-D slice overlay and 3-D) | fmri, fmr lab, anatomy, brain mapping, data analysis, independent component analysis, neuroimaging, image processing, statistical analysis, data visualization, matlab |
is related to: FreeSurfer has parent organization: Swartz Center for Computational Neuroscience |
NIMH 5RO1MHO61619-03 | nif-0000-00077 | SCR_005164 | 2025-05-12 11:07:03 | 3 | ||||||||
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PHYLOViZ Resource Report Resource Website 50+ mentions |
PHYLOViZ (RRID:SCR_024162) | software resource, software toolkit, software library | Platform independent JAVA software for analysis of sequence based typing methods that generate allelic profiles and their associated epidemiological data.Phylogenetic inference and data visualization for sequence based typing methods. | JAVA, phylogenetic inference, data visualization, sequence based typing methods, generate allelic profiles and their associated epidemiological data, | is listed by: Debian | PMID:22568821 | Free, Available for download, Freely available, | https://sources.debian.org/src/phyloviz-core/ | SCR_024162 | 2025-05-12 11:24:49 | 52 | ||||||||
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Divvy Resource Report Resource Website 1+ mentions |
Divvy (RRID:SCR_006336) | Divvy | software application, data visualization software, source code, data analysis software, data processing software, software resource | 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. | data analysis, cluster, machine learning, visual analytics, data visualization, plugin, k-means, principal component analysis, scatter plot | has parent organization: University of California at San Diego; California; USA | NSF 0963071 | MIT License | nlx_152038 | SCR_006336 | 2025-05-13 11:14:00 | 1 | |||||||
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GenomeCompiler Resource Report Resource Website 10+ mentions |
GenomeCompiler (RRID:SCR_013988) | software application, data visualization software, collaboration tool, data processing software, software resource, data management software | 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. | software application, genetic engineering, genomic maniplation, tool, data visualization, data management, collaboration, platform |
is used by: Addgene is used by: Sigma-Aldrich is used by: University of California at Berkeley; Berkeley; USA is used by: Stanford University; Stanford; California is used by: Harvard University; Cambridge; United States is used by: Massachusetts Institute of Technology; Massachusetts; USA; is listed by: Connected Researchers is related to: Addgene is related to: Sigma-Aldrich is related to: Connected Researchers |
Free, Available to the research community | SCR_013988 | 2025-05-13 11:16:41 | 10 | ||||||||||
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Tableau Desktop Resource Report Resource Website 10+ mentions |
Tableau Desktop (RRID:SCR_013994) | software application, data visualization software, data analytics software, data processing software, software resource | 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. | data analytics, data visualization, drag and drop |
is used by: Merck is listed by: Connected Researchers is related to: Connected Researchers |
Free ; Price (for certain editions and packages) |
Free, Fee (for certain editions and packages) | http://www.tableau.com | SCR_013994 | 2025-05-13 11:16:41 | 15 | ||||||||
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ERPwavelab Resource Report Resource Website 1+ mentions |
ERPwavelab (RRID:SCR_014106) | software application, data visualization software, data analysis software, software toolkit, data processing software, software resource | 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. | software toolbox, data analysis, data visualization, eeg data, meg data, plugin, time frequency domain, fourier time domain analysis, temporal wavelet analysis |
is used by: EEGLAB is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Technical University of Denmark; Lyngby; Denmark |
Open source | http://www.erpwavelab.org | SCR_014106 | 2025-05-13 11:16:43 | 8 | |||||||||
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Py3DN Resource Report Resource Website 1+ mentions |
Py3DN (RRID:SCR_014511) | software application, 3d visualization software, data visualization software, data analysis software, data processing software, software resource | 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. | morphometric analysis, morphometry, data visualization, 3d, neuron, neuronal structure | DOI:10.1007/s12021-013-9188-z | Open source, Available for download | SCR_014511 | 2025-05-13 11:16:50 | 1 | ||||||||||
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SciDAVis Resource Report Resource Website 50+ mentions |
SciDAVis (RRID:SCR_014643) | software application, data visualization software, data analysis software, data processing software, software resource | 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. | data analysis, data visualization, plot, easy user interface, interactive, software application | Free, Available for download, Runs on GNU/Linux, Runs on Windows, Runs on MacOS X | SCR_014643 | Scientific Data Analysis and Visualization (SciDAVis) | 2025-05-13 11:16:53 | 89 | ||||||||||
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MetaMapR Resource Report Resource Website 1+ mentions |
MetaMapR (RRID:SCR_014685) | software resource, software application, data visualization software, data processing software | 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. | metabolomics, metabolomics tool, enzymatic transformations, metabolite structural similarity, mass spectral similarity, metabolic networks, data visualization, bio.tools |
is listed by: Metabolomics Workbench is listed by: Debian is listed by: bio.tools |
PMID:25847005 | Open source | biotools:metamapr | https://bio.tools/metamapr | SCR_014685 | 2025-05-13 11:16:54 | 7 | |||||||
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Multi-omics Visualization Platform Resource Report Resource Website 1+ mentions |
Multi-omics Visualization Platform (RRID:SCR_018077) | MVP | software application, data visualization software, data analysis software, data processing software, software resource | 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. | Proteogenomics, data, multi-omics, mass spectrometry, proteomics, genomics, transcriptomics, Galaxy Project, data visualization, bio.tools |
is listed by: bio.tools is listed by: Debian |
NIH U24 CA199347 | Free, Available for download, Freely available | biotools:mvp_a | http://galaxyp.org https://bio.tools/mvp_a |
SCR_018077 | Multi-omics Visualization Platform, Galaxy MVP | 2025-05-13 11:18:29 | 1 | |||||
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PlotsOfData Resource Report Resource Website 10+ mentions |
PlotsOfData (RRID:SCR_018333) | software resource, service resource, analysis service resource, data access protocol, production service resource, data analysis service, web service | 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. | Data visualization, data statistics, comparison between samples, plot, graph, data |
uses: Shiny uses: R Project for Statistical Computing uses: RStudio uses: ggplot2 uses: dplyr uses: tidyr is related to: BoxPlotR |
PMID:30917112 | Free, Freely available | https://github.com/JoachimGoedhart/PlotsOfData | SCR_018333 | 2025-05-13 11:18:34 | 30 | ||||||||
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Gnumeric Resource Report Resource Website 1+ mentions |
Gnumeric (RRID:SCR_018462) | software application, data visualization software, data analytics software, data analysis software, data processing software, software resource | Software tool as open source spreadsheet program that is part of GNOME Free Software Desktop Project. Can do some statistical analysis such as Student t-tests. Spreadsheet application that replicates basic features of popular commercial programs like Microsoft Excel. | Spreadsheet program, statistical analysis, Student t-test, data analysis, data visualization, data processing | Free, Available for download, Freely available | SCR_018462 | , Gnumeric Spreadsheet, Gnumeric version 1.0 | 2025-05-13 11:18:36 | 2 | ||||||||||
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CurveFitter Resource Report Resource Website 1+ mentions |
CurveFitter (RRID:SCR_018461) | software resource, data analysis software, software application, data processing software | Software tool for growth curve fitting and visualization. Program allows to fit growth curve using simple GUI or advanced scripting environment. Used to fit growth curves generated for data collected in microtiter plates or elsewhere. | Growth curve fitting, data visualization, data, microtiter plate data, microbiology, microtiter plate | Free, Available for download, Freely available | https://archive.codeplex.com/?p=curvefitter | SCR_018461 | curvefitter | 2025-05-13 11:18:36 | 3 | |||||||||
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Affymetrix Transcriptome Analysis Console Software Resource Report Resource Website 10+ mentions |
Affymetrix Transcriptome Analysis Console Software (RRID:SCR_018718) | Affymetrix TAC | software application, data visualization software, data analysis software, data processing software, software resource | Software to generate differential expression analysis and visualization for easy interpretation. Takes normalized and summarized data from Affymetrix Expression Console software to next level, providing differential expression analysis and visualization for easy interpretation. | Affymetrix, transcriptome analysis, analysis console, differential expression analysis, data visualization |
works with: GeneAtlas System works with: GeneAtlas System |
Restricted | SCR_018718 | 2025-05-13 11:18:41 | 13 | |||||||||
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MSTools Resource Report Resource Website 10+ mentions |
MSTools (RRID:SCR_018657) | software resource, service resource, data access protocol, web service | Web based application for visualization and presentation of HXMS data. Comprises tools helping in preparation of H/D experiments as well as tools for turning simple tables with data on H/D exchange into different ways of representation. | Hydrogen, deuterium, exchange data, data visualization, HXMS data, data calculation, graphical representation | DOI:10.1016/j.ijms.2010.07.030 | Free, Freely available | SCR_018657 | 2025-05-13 11:18:40 | 10 | ||||||||||
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GigaSOM.jl Resource Report Resource Website 1+ mentions |
GigaSOM.jl (RRID:SCR_019020) | software resource, software application, data visualization software, data processing software | Software tool for huge scale, high performance flow cytometry data clustering and visualization in Julia. High performance clustering and visualization of huge cytometry datasets. | Flow cytometry data, flow cytometry data clustering, data clustering, data visualization, Julia, datasets, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1101/2020.08.03.234187 | Free, Available for download, Freely available | biotools:GigaSOM.jl | https://bio.tools/GigaSOM.jl | SCR_019020 | 2025-05-13 11:18:49 | 2 |
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