1 - 31 of 31 results

Web-igloo

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Visualizes multivariate data in a 2D chart of multiple quantitative variables represented as anchors on a semicircle. Web-Igloo not only identifies clusters in data but also allows to infer the features responsible for formation of the clusters. Projected data points can be easily mapped to class label information using a simple metadata file. View from among a list of examples or upload data into tool’s server to generate a customized layout. Web-Igloo plots multi-dimensional data keeping all the features intact without any feature decomposition. Web-Igloo is an interactive web version of Igloo-plot.

Taxonomer

An ultrafast web-tool for comprehensive metagenomics data analysis and interactive results visualization. Taxonomer is unique in providing integrated nucleotide and protein-based classification and simultaneous host messenger RNA (mRNA) transcript profiling. Using real-world case-studies, we show that Taxonomer detects previously unrecognized infections and reveals antiviral host mRNA expression profiles. Taxonomer enables rapid, accurate, and interactive analyses of metagenomics data on personal computers and mobile devices.

BURRITO / Browser Utility for Relating micRobiome Information on Taxonomy and functiOn

Allows visual analysis of the relationships between taxonomic and functional abundances across microbiome samples. BURRITO provides an interface for exploring taxonomic and functional abundances independently. It can display the links between these two microbiome facets and highlighting the share of each function’s total abundance that is attributed to each taxon. This tool can be useful for microbial ecology researches.

Krona

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Allows hierarchical data to be explored with zoomable pie charts. Krona aims to answer questions regarding the relative abundance of taxa across multiple levels of the hierarchy simultaneously. The software supplements existing metagenomic visualizations by creating clearer depictions of abundance estimates and by enabling in-depth understanding of the underlying classifications. Windows and Mac users can create Krona charts with Microsoft Excel using Krona Excel template.

VAMPS / Visualization and Analysis of Microbial Population Structures

An integrated collection of tools with which researchers can visualize and analyze data for microbial population structures and distributions. The project includes visualization tools such as heat maps that simultaneously compare the taxonomic distributions of multiple datasets and 3-D charts of the frequency distributions of 16S rRNA tags. Analytical tools include Chao diversity estimates and rarefaction curves. As a service to the community, researchers have the opportunity to upload their own data to the site for private viewing with the full range of data and analysis tools. Public data can be downloaded for further analysis locally.

MetaCoMET / Metagenomics Core Microbiome Exploration Tool

A web platform that enables the discovery and visualization of the core microbiome and provides a comparison of the relative abundance and diversity patterns between subsets of samples within a microbiome dataset. MetaCoMET provides an efficient and interactive graphical interface for analyzing each subset defined by the union or disjunction of groups within the Venn diagram, and includes a graphical taxonomy summary, alpha diversity metrics, Principal Coordinate analysis, abundance-based heatmaps, and a chart indicating the geographic distribution of each sample.

GraPhlAn / Graphical Phylogenetic Analysis

A tool for compact and publication-quality representation of circular taxonomic and phylogenetic trees with potentially rich sets of associated metadata. GraPhlAn was developed primarily for microbial genomic and microbiome-related studies in which the complex phylogenetic/taxonomic structure of microbial communities needs to be complemented with quantitative and qualitative sample-associated metadata. It is composed by two Python modules: one for drawing the image and one for adding annotations to the tree. GraPhlAn exploits the annotation file to highlight and personalize the appearance of the tree and of the associated information. The annotation file does not perform any modifications to the structure of the tree, but it just changes the way in which nodes and branches are displayed. GraPhlAn has been developed as an open-source command-driven tool in order to be easily integrated into complex, publication-quality bioinformatics pipelines. It can be executed either locally or through an online Galaxy web application.

ASAR / Advanced metagenomic Sequence Analysis in R

Allows users to select, aggregate, and visualize metagenomic data. ASAR enables researchers to develop a meaningful view of their data. The software consists of a main panel with seven tabs and a control panel, which provides a set of parameter selectors for controlling the displayed tab content. It can perform taxonomic and functional analyses simultaneously, by subsetting and aggregating abundance data at various levels of taxonomic and functional hierarchies.

Metaviz

Provides a novel navigation tool for exploring hierarchical feature data that is coupled with multiple data visualizations including heatmaps, stacked bar charts, and scatter plots. Metaviz is a web browser-based tool for interactive visualization and exploration of metagenomic sequencing data. It also supports common data exploration techniques, including PCA scatter plots to interpret variability in the dataset and alpha diversity boxplots for examining ecological community composition.

Elviz / Environmental Laboratory Visualization

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An interactive web-based tool for the visual exploration of assembled metagenomes and their complex metadata. Elviz allows scientists to navigate metagenome assemblies across multiple dimensions and scales, plotting parameters such as GC content, relative abundance, phylogenetic affiliation and assembled contig length. Furthermore Elviz enables interactive exploration using real-time plot navigation, search, filters, axis selection, and the ability to drill from a whole-community profile down to individual gene annotations. Thus scientists engage in a rapid feedback loop of visual pattern identification, hypothesis generation, and hypothesis testing.

EMPeror

An open source and web browser enabled tool with a versatile command line interface that allows researchers to perform rapid exploratory investigations of 3D visualizations of microbial community data, such as the widely used principal coordinates plots. EMPeror includes a rich set of controllers to modify features as a function of the metadata. By being specifically tailored to the requirements of microbial ecologists, EMPeror thus increases the speed with which insight can be gained from large microbiome datasets.

POMO / Plotting Omics analysis results for Multiple Organisms

Assists for omics data analysis. POMO is a web application that allows users to display and select the genome-wide networks in the context of chromosomal locations as well as multiple network layouts. This software features the processing of any heterogeneous omics data analysis association results for many organisms. Users can also visualize genomic associations between two related organisms or two distinct strains within the same POMO supported organism.

CoVennTree / Comparative weighted Venn Tree

Simultaneously compares up to three multifarious datasets by aggregating and propagating information from the bottom to the top level and produces a graphical output in Cytoscape. The underlying concept of CoVennTree is to bring information from the leaf level up to the root node while maintaining the properties of the content of every dataset. With the introduction of weighted Venn structures, the amounts and relationships of data associated with different conditions can be correlated and simultaneously aggregated without losing relevant information. CoVennTree has been integrated into the Galaxy ToolShed and can be directly downloaded and integrated into the user instance.

MGAviewer / MetaGenomic Alignment Viewer

A visualization tool for analysis and comparison of mapping data, with a focus on virus and microorganisms NGS data. Compared to current visualization methods, which are often genome browsers, our method has unique advantages. MGAviewer does not relay on a web server or a heavy relational database, which are expensive to maintain and update. This visualization tool solely uses a web browser, so it is platform-independent and requires no software installation. It analyzes mapping data from a local computer and it can be much faster than web-based genome browser for interactive use. Due to these features, this tool can be very easily applied by individual labs for their routine analysis of mapping data.

Community-analyzer

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A GUI-based comparative metagenomic analysis application which implements a correlation-based graph layout algorithm that not only facilitates a quick visualization of the differences in the analyzed microbial communities (in terms of their taxonomic composition), but also provides insights into the inherent inter-microbial interactions occurring therein. Notably, this layout algorithm also enables grouping of the metagenomes based on the probable inter-microbial interaction patterns rather than simply comparing abundance values of various taxonomic groups. In addition, the tool implements several interactive GUI-based functionalities that enable users to perform standard comparative analyses across microbiomes.

MetaSee

Obsolete
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An extendable toolbox to facilitate the interactive visualization of metagenomic samples of interests. MetaSee includes: (I) a core visualization engine that is composed of different views for comparison of multiple samples: Global view, Phylogenetic view, Sample view and Taxa view, as well as link-out for more in-depth analysis; (II) front-end user interface with real metagenomic models that connect to the above core visualization engine and (III) open-source portal for the development of plug-ins for MetaSee. MetaSee is not only for metagenomics, it is a flexible framework that can also take other dataset of tree structure as input and give beautiful visualization results.

VITCOMIC / VIsualization tool for Taxonomic COmpositions of MIcrobial Community

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Allows visualization of overall taxonomic composition of 16S rRNA gene-based microbial community analysis data. VITCOMIC produces figures that contain four categories of dot size that indicate the relative abundance of the sample sequence. It utilizes the 16S rRNA gene sequences from 601 genome-sequenced bacteria as references. This tool facilitates an intuitive understanding of differences in community structure between samples.

MetaLook

Obsolete
Offers a three-dimensional user interface to interactively visualise DNA sequences on a world map, based on a centralised georeferenced database. MetaLook is a software for visualisation and analysis of marine ecological genomic and metagenomic data with respect to habitat parameters. It allows scientists to investigate sequence data in their environmental context and to explore correlations between genes and habitat parameters. This software is a step towards the creation of specialised tools to study constrained distributions and habitat specificity of genes correlated with specific processes.