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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.
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.
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.
bdvis
Facilitates efforts to understand the gaps and strengths of primary biodiversity record data with quick and useful visualization functions. The package’s functions may be classified broadly as follows: (1) helper functions to convert data to the correct format to be used in bdvis, and to enrich an initial data set with additional data (like higher taxonomy and grid identifiers); (2) summary tables; (3) geographic, temporal and taxonomic visualizations; and (4) other miscellaneous graphs and charts.
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.
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.
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.
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.
Community-analyzer
Obsolete
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.
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.
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