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An open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization. Cytoscape core distribution provides a basic set of features for data integration, analysis, and visualization. Additional features are available as Apps (formerly called Plugins). Apps are available for network and molecular profiling analyses, new layouts, additional file format support, scripting, and connection with databases.
Cytoscape Web
Allows network visualization. Cytoscape Web can be customized and incorporated into any web site. It allows the client application to define a network of nodes and edges and customize their attributes. The tool permits to dynamically change node and edge visual styles, using any of the following methods: specifying default visual properties for all elements; mapping node and edge attributes to visual styles; and overriding default or mapped styles by setting a bypass style.
JDotter / Java-Dotter
Runs as a client–server application and can send new sequences to the Dotter program for alignment as well as rapidly access a repository of preprocessed dotplots. JDotter is a platform-independent Java interactive interface for the Linux version of Dotter, a widely used program for generating dotplots of large DNA or protein sequences. It interfaces with a sequence database or file system to display supplementary feature data. Thus, JDotter greatly simplifies access to dotplot data in laboratories that deal with large numbers of genomes and have a multi-platform organization.
An R package called GOplot, based on ggplot2, for enhanced graphical representation. Our package takes the output of any general enrichment analysis and generates plots at different levels of detail: from a general overview to identify the most enriched categories (bar plot, bubble plot) to a more detailed view displaying different types of information for molecules in a given set of categories (circle plot, chord plot, cluster plot). The package provides a deeper insight into omics data and allows scientists to generate insightful plots with only a few lines of code to easily communicate the findings.
Analyzes data using predefined analysis scenarios via a graphical user interface (GUI). RReportGenerator is a user-friendly portal for automatic routine analysis using the statistical platform R and Bioconductor. It allows calling R and executing the code from a user-selected pre-defined ‘Analysis Scenario’ for automatically generating reports. RReportGenerator can be used in a wide range of routine analysis cases in clinical and biological research where the aim and structure of the experiments change rarely, like automatic quality control (e.g. of Affymetrix arrays) or analyzing high content screening (HCS) plates.
imDEV / interactive modules for Data Exploration and Visualization
Unites the Microsoft Excel spreadsheet and allows users to perform multivariate analysis and visualization. imDEV simplifies multivariate data interpretation by integrating dynamic data visualization with univariate statistics, dimensional reduction methods, predictive modeling and network analyses tools. In summary, this tool consists of a Visual Basic for Applications (VBA)-based graphical user interface that accesses R-based visualizations and statistical algorithms, that operate on data stored within and returned to named ranges or worksheets within Excel.
TikZ and PGF
TeX packages for creating graphics programmatically. TikZ is build on top of PGF and allows you to create sophisticated graphics in a rather intuitive and easy manner. TikZ offers all the advantages of the “TEX-approach to typesetting” for graphics: quick creation of simple graphics, precise positioning, the use of macros, often superior typography. PGF is a TeX macro package for generating graphics. It is platform- and format-independent and works together with the most important TeX backend drivers, including pdftex and dvips.
Provides a unique way to integrate and optimize R code for data-visualization with web-based real-time manual optimization with computational pipelines. VennDiagramWeb facilitates the creation of both Venn and Euler diagrams for computational biologists. This tool is meant to integrate seamlessly into scientific plot generation workflows. To this end, it included several key features: data file uploads, access to underlying R code (user can access the generated R code to reproduce the plot as it appears on screen), image downloads and multiple workspaces (the web application has an interface for creating and switching between tabs). Users can modify the parameters of the Venn diagram function using the sidebar, and the resultant plot is generated instantly in the center panel.
Generates interactive graphs in R. RJSplot contributes to the development of interactive visualization packages in R oriented toward computational biology research. The software implements 16 interactive graphical representations. It provides a dynamic and customizable visualization and allows actions such as browsing, movement, zoom adjustment, viewing values, or identifying variables. It can be used to allow a comprehensive visualization of information and an improved diffusion of scientific results.
Allows users to design customized visualizations without the need to write code. Lyra is an interactive design environment for custom visualization that permits adding graphical marks to a canvas and associating data fields. The software provides a data pipeline interface that enables data transformation and advanced layout algorithms. It represents visualizations using the Vega visualization grammar, allowing users to publish on the web, share and repurpose visualizations. The software thus contributes a novel interactive system for visual specification of grammar-driven visualizations.
Provides a streamlined visualization workflow and sleek user interface, aimed at enabling novel explorations of large biological datasets as part of the downstream data analysis workflow. Phinch is an interactive, exploratory data visualization tool designed to facilitate the analysis of -omic datasets. It was developed to encourage researchers and public audiences to interact with and explore large -omic datasets, regardless of computational skill level. This framework also promotes effective and efficient scientific research by providing an intuitive and easy way to filter data, identify biological patterns, and export publication quality graphics.
Spdep / Spatial Dependence
Provides several functions to generate spatial weights matrix objects from polygon contiguities. Spdep enables the summarization of point patterns by distance and tessellations and allows their use in spatial data analysis. This software permits regional aggregation by minimum spanning tree and includes a collection of tests for spatial autocorrelation such as spatial regression models, saddlepoint approximations, Gearys C, or even Empirical Bayes estimates.
BPG / BoutrosLab.plotting.general
Allows users to produce figures suited for publications. BPG incorporates methods for visualization high-dimensional datasets and generates complex multi-panel figures. The figures created by this software integrates into R-based statistical pipelines like Bioconductor. A variety of chart-types is available to match the diversity of datatypes in research publications. A 45-color palette is available with optimized color schemes to ease the interpretation.
An online tool for quickly and easily generating graphs and analysis from small bioinformatics files such as BED, expression and VCF files. You can rapidly upload multiple files via drag & dropping them onto the page, or using the "upload" buttons. BioGraphServ will detect the file type, and generate default analysis and graphs. Graphs can be customised and downloaded in multiple formats, and data from multiple files combined for download or further analysis via the "Combo" functionality.
GRAL / GRAphing Library
Enables users to generate graphs and charts. GRAL is a free to use and lightweight library for displaying plots (graphs, diagrams and charts). This library has many features and provides (i) various axis types: linear axes, logarithmic axes, arbitrary number of axes, (ii) many different plot types: xy/scatter plot, bubble plot, line plot, area plot, bar plot, pie plot, donut plot, box-and-whisker plot, raster plot, (iii) data processing and filtering (smoothing, rescaling, statistics, histograms) and many others.
Produces for researchers publication-quality figures in a variety of hardcopy formats and interactive environments across platforms. Matplotlib is conceptually divided into three parts: (1) the pylab interface user to create plots with code quite similar to MATLAB; (2) the frontend or API is the set of classes that do the heavy lifting, creating and managing figures, text, lines, plots; and (3) the backends are device-dependent drawing devices that transform the frontend representation to hardcopy or a display device.
Provides features for displaying interactive diagrams and graphs. Mxgraph is a family of libraries providing a range of commonly required functionalities to draw, able to interact with and associate a context with a diagram. It also offers a basic set of implementations of graph layout algorithms including trees, force-directed and hierarchical layouts. Developers can interact with the mxgraph generated diagrams through a series of actions like for instance dragging and cloning cells, resizing and reshaping, connecting and disconnecting, drag and dropping, or in-place editing.
Explores relationships within and among related datasets. Glue is a python project to link visualizations of scientific datasets across many files. This library was designed with “data-hacking” workflows in mind. With Glue, users can create scatter plots, histograms and images (2D and 3D) of their data. It is focused on the brushing and linking paradigm, where selections in any graph propagate to all others. This package uses the logical links that exist between different data sets to overlay visualizations of different data, and to propagate selections across data sets.
Enables developers to generate graphs and charts. JFreeChart is a free to use Java library that can generate common chart types including pies (2D and 3D), bars, bubbles, scatters (2D and 3D), histograms and Gantt charts. It also provides an application programming interface (API) that supports interactive drawing features such as tool tips, color gradients, drop-shadows and zooming. This software is compatible with most of Java Swingbased applications and is also integrated into the MetaFIND tool.
Offers an interactive R/browser plotting. BrowserVizDemo is an early, simple example of how to create useful interactive graphics in a class derived from BrowserViz. This package could evolve to be a drop-in replacement for the R base "plot" function, for plotting xy values. It has the additional virtue of full interactivity on the plotting surface, which is here an HTML5/d3 canvas. Manually selected points on that canvas, for example, can be queried in R. This may facilitate exploratory data analysis.
Draws a non-overlapping wordmatch dotplot of two sequences. dotpath uses the same algorithm as diffseq and dottup for finding a minimal set of exact matches between two sequences. It finds all identical words of size -wordsize or greater in the two sequences. It then reduces the matches found to the minimal set of matches that do not overlap. This set is rendered as lines in the dotplot. For similar sequences, dotpath provides a convenient way to find a path that aligns the two sequences well.
Draws a chaos game representation (CGR) plot for a nucleotide sequence. A CGR plot represents a nucleotide sequence as a square box with an A, G, C, or T nucleotide at each corner. The box contains dots, each one representing a dinucleotide. All overlapping dinucleotides from the start to the end of the sequence are plotted. Regions which are devoid of dots (or heavily covered with dots) indicate short sequence motifs that are unusually infrequent (or frequent). CGR plots depict base composition and sequentiality and is a unique visual representation of a sequence that complements more traditional linear representations.
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