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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.
GenPlay
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Provides an analyser and browser tool for data expressed in multiple genomic coordinate systems. GenPlay can display RNA-seq, ChIP-seq, Methyl-seq, TimEX-seq and a variety of DNA sequence and annotation tracks. This software can used also for the evaluation of data aligned on custom genomes and offers a library of operations to process raw data. It enables data export into any of the coordinate systems that makeup the meta-reference genome.
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.
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.
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.
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.
Apollo
A browser-based genome editor that supports geographically dispersed researchers whose work is coordinated through automatic synchronization. The overall platform is currently comprised of a visualization component - JBrowse, and an editing and user authentication component - Apollo. With Web Apollo the task of manual curation is spread out among many hands and eyes, enabling the creation of virtual research networks of researchers linked by a common interest in a particular organism or population.
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.
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.
PGB / Personal Genome Browser
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.
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.
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.
GenomeGraphs
Facilitates analysis and visualization of mRNA-Seq data. GenomeGraphs is a visualization tool that allows complex customization to facilitate a more complete integration and representation of genomic datasets. The software relies on biomaRt package to retrieve genomic annotation information on-line from Ensembl using BioMart web services. GenomeGraphs can plot together several types of data using the same genome coordinate system. It also allows users to create custom annotation tracks.
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.
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.
GenomePlot
Displays a wide variety of data on a single genomic backbone in either a circular or linear format. GenomePlot is a visualization tool that allows users to zoom to the desired view of the data and to print or save the image to a file for producing publication quality illustrations. The software has been used to generate displays for several genomes, including Methanobacterium thermoautotrophicum, Helicobacter pylori, Clostridium acetolbutylicum, and Agrobacterium tumefaciens.
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.
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.
Chromozoom
An interactive genome browser on the web for both curated and custom data, with a focus on ease of use and flexibility. Chromozoom enables rapid and simultaneous exploration of curated, experimental and personal genomic datasets. It pre-renders and caches general-use tracks into tiled images on the server and serves them in an interactive web interface with inertial scrolling and precise, fluent zooming via the mouse wheel or trackpad. Custom tracks in several formats can be rendered by client-side code alongside the pre-rendered tracks, minimizing server load because of user-specific rendering and eliminating the need to transmit private data.
UK10K Genome Browser
Exploits the key basic features of the Biodalliance Genome Browser. UK10K Genome Browser provides an intuitive and efficient platform to access association statistics for common, low frequency and rare variants against a large number of human phenotypic traits. As efforts progress to systematically map the contribution of human genetic variation to healthy and diseased phenotypes, and to integrate it with genome functional resources, the development of UK10K Genome Browser is essential enabling instruments for the integration and cross-validation of genetic discoveries within the scientific community.
HUGIn / Hi­C Unifying Genomic Interrogator
Visualizes Hi-C data generated from 21 human primary tissues and cell liens. HUGIn a web browser that enables assessment of chromatin contacts both constitutive across and specific to tissue(s) and/or cell line(s) at any genomic loci, including GWAS SNPs, eQTLs and cis-regulatory elements, facilitating the understanding of both GWAS and eQTLs results and functional genomics data. HUGIn also hosts gene expression and a rich collection of epigenomic data, including typical and super enhancers.
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Islet Regulome Browser
Allows fast access and exploration of pancreatic islet epigenomic and transcriptomic data produced by different labs worldwide. Islet Regulome Browser allows uploading custom tracks as well as providing interactive access to a wealth of information including Genome-Wide Association Studies (GWAS) variants, different classes of regulatory elements, together with enhancer clusters, stretch-enhancers and transcription factor binding sites in pancreatic progenitors and adult human pancreatic islets. This application facilitates the access to pancreatic islet public genomic datasets providing a major boost to functional genomics studies in glucose metabolism related traits including diabetes.
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