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Circos
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Displays large volumes of genomic rearrangement data. Circos is a visualization tool that applies a circular ideogram layout to display relationships between genomic intervals. The software provides a scalable means to illustrate relationships between genomic positions and is designed to allow flexible and easy rearrangement of elements in the image. It also contains several tools to help analyze, filter, and format data.
I-PV / Interactive Protein Sequence Visualization
Allows to visualize user supplied protein sequence, conservation and single nucleotide variant (SNV) in a live presentable format. I-PV is an interactive data visualization software that comes with tools to extract sequence, conservation, specific features and SNVs between user defined regions in a formatted text layout with user defined number of items per line. An add-on included in the software allows to visualize point mutations in user supplied variation/vcf files.
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.
BioCircos.js
An interactive and lightweight JavaScript library especially for biological data interactive visualization. BioCircos.js is not a web application for end-users but a JavaScript library for programmers. Developers need to write code around BioCircos.js to build web applications. BioCircos.js provides flexible and powerful functionality for the development of web-based circular visualization tools for multi-faceted biological data. These applications will be developed as plugins to simplify the process of generating circular image.
J-Circos
An interactive visualization tool that can plot Circos figures, as well as being able to dynamically add data to the figure, and providing information for specific data points using mouse hover display and zoom in/out functions. J-Circos uses the Java computer language to enable it to be used on most operating systems. Users can input data into J-Circos using flat data formats, as well as from the GUI. J-Circos will enable biologists to better study more complex chromosomal interactions and fusion transcripts that are otherwise difficult to visualize from next-generation sequencing data.
CircosVCF
Generates circos visualization of whole genome variation information. CircosVCF is an interactive user-friendly web service. The strength of this web application is in its ability to present in an intuitive graphical manner a comparison of variation distribution between multiple genomes. It provides a birds-eye view of the genomic relatedness of individuals based on whole genome single nucleotide polymorphism (SNP) information, but also enables the detection of specific meaningful SNPs regions, as well as their host genes which later on can be further analyzed using various tools.
OmicCircos
Allows creation of circular plots. OmicCircos illustrates genomic data analyses and also carries out statistical, analyses that can be combined to generate publication-ready circular plots for a wide range of data types. The software offers four capabilities: (1) independent track plotting and modification, (2) integrated statistical analysis and the concomitant display, (3) a zoom function, and (4) storage of genomic annotations and alignments. It allows to visualize several genomic variations: mutation patterns, copy number variations (CNVs), expression patterns, and methylation patterns.
myCircos
A web application that facilitates the generation of Circos plots by providing an intuitive user interface, adding interactive functionalities to the representation and providing persistence of previous requests. myCircos provides useful functionalities such as: a database that stores previously generated plots, and interactive SVG (Scalable Vector Graphics) output. Extending the typical and static graphical output, users can interrogate their plots using the interface, directly within their web-browser. Being flexible and user-friendly but still exposing the key features of original command-line tool, it removes some of the challenges associated with Circos plot creation.
Circa
Allows user to make circos plots from genomic data. Circa can plot any genomic data from any organism and any reference genome. Ideal data for plotting in Circa includes variant calls, copy number profiles, and any genomic features like repeats, genes, or the plethora of data available in ENCODE or through the UCSC genome browser. It permits to specify the chromosome colors using the easy color picker or by entering a list of HEX codes. Circa is not limited to the number of tracks or datasets user can plot in.
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