1 - 50 of 140 results

IGV / Integrative Genomics Viewer

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Enables users to explore large, integrated genomic datasets. IGV provides next-generation sequencing (NGS) data visualization and provides features for identification of sequencing and analysis artifacts, leading to errant single-nucleotide variant (SNV) calls, as well as support for viewing large-scale structural variants (SV) detected by paired-end read technology. The software also includes features to support third-generation long-read sequencing technologies. Several IGV features have been developed to aid manual review of aligned reads.

TnT

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A set of libraries aimed at creating powerful tree- and track-based visualisations for the web. Its modularity and rich API facilitate the development of many different visualisations ranging from simple species trees to complex visualisations comprising per-node data annotations or even simple genome browsers. The TnT libraries have been written in Javascript using the D3 library as its main dependency. It uses SVG to render all the visual elements in the browser.

GenPlay

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An analyzer and browser for high-throughput data. GenPlay recognizes a wide variety of common genomic data formats from microarray- or sequencing-based platforms and offers a library of operations (normalization, binning, smoothing) to process raw data into visualizable tracks. GenPlay displays tracks adapted to summarize gene structure, gene expression, repeat families, CPG islands, etc. as well as custom tracks to show the results of RNA-Seq, ChIP-Seq, TimEX-Seq and single nucleotide polymorphism (SNP) analysis. GenPlay can generate statistics (minimum, maximum, SD, correlation, etc.).

IGB / Integrated Genome Browser

An easy-to-use, highly customizable genome browser you can use to view and explore genomic data and annotations, especially RNA-Seq and ChIP-Seq data sets. IGB supports real-time zooming and panning through a genome; layout of genomic features and datasets in moveable, adjustable tiers; incremental or genome-scale data loading from remote web servers or local files; and dynamic manipulation of quantitative data via genome graphs. We enhanced IGB's ability to consume data from diverse sources, including Galaxy, Distributed Annotation, and IGB-specific Quickload servers. To support future visualization needs as new genome-scale assays enter wide use, we transformed the IGB codebase into a modular, extensible platform for developers to create and deploy all-new visualizations of genomic data.

JGI Genome Portal / Joint Genome Institute Genome Portal

Gives access to genome sequences and annotations, and allows exploration of genomic data. JGI Genome Portal furnishes worldwide statistics on the usage of the JGI resources and the information about the latest genome releases and new tool development. It can automatically generate and monitor BioSample and BioProject submissions to NCBI. This database permits users to access to other resources such as the Genomes OnLine Database (GOLD).

Savant

Enables visualization and navigation of reference genomes and corresponding genomic data sets. Savant is a genome browser that supports a wide range of file formats, as well as the use of remote files and datasources. Navigation to genomic regions of interest is assisted through textual search and bookmarks. The software delivers creative visualization representations for high-throughput sequencing (HTS) data and a plugin architecture that provides the opportunity to incorporate any computational tool within a visual environment.

Epiviz

An interactive visualization tool for functional genomics data. Epiviz supports genome navigation like other genome browsers, but allows multiple visualizations of data within genomic regions using scatterplots, heatmaps and other user-supplied visualizations. Epiviz sets a precedent for genomic data analysis collaborative workflows by enabling reproducible and shareable steps, and allowing custom user code to be dynamically incorporated, while guaranteeing the security and integrity of user data.

Artemis

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A free genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation. Artemis has support for various standard file formats including BAM and VCF, in addition to user-defined input files. These formats can support data from many different types of sequencing platforms. Therefore, Artemis has the potential to visualize and investigate sequencing data from numerous sequencing technologies.

ChAsE / Chromatin Analysis and Exploration

A cross-platform desktop application developed for interactive visualization, exploration and clustering of epigenomic data such as ChIP-seq experiments. ChAsE is designed and developed in close collaboration with several groups of biologists and bioinformaticians with a focus on usability and interactivity. Data can be analyzed through k-means clustering, specifying presence or absence of signal in epigenetic data, and performing set operations between clusters. Results can be explored in an interactive heat map and profile plot interface and exported for downstream analysis or as high quality figures suitable for publications.

GenVisR

Provides a user-friendly, flexible, and comprehensive suite of tools for visualizing complex genomic data in three categories (small variant, copy number alteration, and data quality). By leveraging the abilities of ggplot2 it confers a level of customizability not previously possible. Virtually any aspect of a plot can be changed simply by adding an additional layer onto the graphical object. Thus, GenVisR allows for publication quality figures with a minimal amount of required input and data manipulation while maintaining a high degree of flexibility and customizability.

Map Viewer

Provides special browsing capabilities for a subset of organisms in Entrez Genomes. Map Viewer allows you to view and search an organism's complete genome, display chromosome maps, and zoom into progressively greater levels of detail, down to the sequence data for a region of interest. The number and types of available maps vary by organism, and are described in the "data and search tips" file for each organism. If multiple maps are available for a chromosome, it displays them aligned to each other based on shared marker and gene names, and, for the sequence maps, based on a common sequence coordinate system.

Dynamix

Enables the parallel inspection of hundreds of genomic data sets. Dynamix automatically displays data tracks with signal within a genomic region of interest. This JBrowse plugin also introduces a new carousel view that optimises screen utilisation by enabling users to independently scroll through groups of tracks. As the user navigates through the genome, Dynamix automatically updates data tracks and limits all manual operations otherwise needed to ad-just the data visible on screen.

caOmicsV

Provides methods under R environment to visualize multidimensional cancer genomic data in two layouts: matrix layout and combined biological network and circular layout. Both layouts support to display sample information, gene expression (e.g., RNA and miRNA), DNA methylation, DNA copy number variations, and summarized data. A set of supplemental functions are included in the caOmicsV package to help users in generation of plot data sets from multiple genomic datasets with given gene names and sample names. Default plot methods for both layouts for easy use are also implemented.

ggbio

A package based on a new methodology to visualize and explore genomics annotations and high-throughput data. ggbio’s plots provide detailed views of genomic regions, summary views of sequence alignments and splicing patterns, and genome-wide overviews with karyogram, circular and grand linear layouts. These plots are specified within a modular framework that enables users to construct plots in a systematic way, and are generated directly from Bioconductor data structures. ggbio provides the tools to create both typical and non-typical biological plots for genomic data, generated from core Bioconductor data structures by either the high-level autoplot function, or the combination of low-level components of the grammar of graphics. Sharing data structures with the rest of Bioconductor enables direct integration with Bioconductor workflows.

DiProGB / Dinucleotide Properties Genome Browser

An easy to use new genome browser that encodes the primary nucleotide sequence by thermodynamical and geometrical dinucleotide properties. The nucleotide sequence is thus converted into a sequence graph. This visualization, supported by different graph manipulation options, facilitates genome analyses, because the human brain can process visual information better than textual information. Also, DiProGB can identify genomic regions where certain physical properties are more conserved than the nucleotide sequence itself. Most of the DiProGB tools can be applied to both, the primary nucleotide sequence and the sequence graph.

myGenomeBrowser

Provides biologists with a way to build, query and share their genome browsers. myGenomeBrowser is a web-based designed to give users more autonomy while simplifying and minimizing intervention from system administrators. Its environment is based on JBrowse and supplemented with various features that are missing from current solutions, such as management of various data sources, mining tools and sharing systems. myGenomeBrowser is provided with an installation script based on the Docker container management system.

pileup.js

A browser-based genome viewer. pileup.js is designed to facilitate the investigation of evidence for genomic variants within larger web applications. It takes advantage of recent developments in the JavaScript ecosystem to provide a modular, reliable and easily embedded library. pileup.js supports visualization of genomic tracks for reference sequences, mapped reads (paired or unpaired), read depth, variants and gene annotations. pileup.js was initially developed to be embedded within the Cycledash variant inspector, but it can be used within any web application.

GTB / Genome Tolerance Browser

Enables users to visualize the similarities and differences between several prediction algorithms. GTB is an online genome browser for visualizing the predicted tolerance of the human genome. It summarizes several in silico prediction algorithms and conservation scores: including 13 genome-wide prediction algorithms and conservation scores, 12 non-synonymous prediction algorithms and four cancer-specific algorithms. The GTB enables differences in prediction to be evaluated and facilitates rapid identification of potential regions of interest. The interactive browser can be used to facilitate the rapid identification of predicted intolerant regions across the genome and can also be used to visualize the concordance and subtle differences between multiple prediction algorithms.

PGB / Personal Genome Browser

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Provides comprehensive functional annotation and visualization for individual genomes based on the genetic-molecular-phenotypic model. Investigators can easily view individual genetic variants, such as single nucleotide variants (SNVs), INDELs and structural variations (SVs), as well as genomic features and phenotypes associated to the individual genetic variants. The PGB especially highlights potential functional variants using the PGB built-in method or SIFT/PolyPhen2 scores.

GCV / Genome Context Viewer

Allows users to explore multiple annotated genomes. GCV is a web-based visual data-mining tool that dynamically identifies syntenic genomic segments. It enables interactive exploration of gene content similarities and differences among distributed collections of annotated genomes. The software can be used as a standalone application or integrated into an existing website. The users can download images of the visualizations and the underlying data for further analysis.

PopHuman

Provides description and analysis of comprehensive human diversity data. PopHuman is a population genomics-oriented genome browser. It represents an update to the 1000GP Phase III (2504 individuals, 26 populations, 84.7 million SNPs), but also dramatic improvements in the amount of data analyzed and browser performance. It also calculates species divergence, which allows the implementation of statistical tests to detect the signature of recurrent natural selection acting over prolonged periods of time.