<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/35400?offset=140 https://bioinformaticsonline.com/bookmarks/view/37230/navigator-network-analysis-visualization-and-graphing-toronto Tue, 03 Jul 2018 05:05:55 -0500 https://bioinformaticsonline.com/bookmarks/view/37230/navigator-network-analysis-visualization-and-graphing-toronto <![CDATA[NAViGaTOR: Network Analysis, Visualization and Graphing Toronto]]> Address of the bookmark: http://142.150.188.236/navigatorwp/

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/38819/upsetr-an-r-package-for-the-visualization-of-intersecting-sets-and-their-properties Mon, 28 Jan 2019 18:38:44 -0600 https://bioinformaticsonline.com/bookmarks/view/38819/upsetr-an-r-package-for-the-visualization-of-intersecting-sets-and-their-properties <![CDATA[UpSetR: An R Package for the Visualization of Intersecting Sets and their Properties]]> UpSetR generates static UpSet plots. The UpSet technique visualizes set intersections in a matrix layout and introduces aggregates based on groupings and queries. The matrix layout enables the effective representation of associated data, such as the number of elements in the aggregates and intersections, as well as additional summary statistics derived from subset or element attributes.

For further details about the original technique see the UpSet website. You can also check out the UpSetR shiny app. Here is the source code for the shiny wrapper.

A Python package called py-upset to create UpSet plots has been created by GitHub user ImSoErgodic.

Address of the bookmark: https://github.com/hms-dbmi/UpSetR/

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/41736/synvisio-an-interactive-multiscale-synteny-visualization-tool-for-mcscanx Sun, 31 May 2020 02:01:14 -0500 https://bioinformaticsonline.com/bookmarks/view/41736/synvisio-an-interactive-multiscale-synteny-visualization-tool-for-mcscanx <![CDATA[SynVisio: An Interactive Multiscale Synteny Visualization Tool for McScanX.]]> SynVisio lets you explore the results of McScanX a popular synteny and collinearity detection toolkit and generate publication ready images.

SynVisio requires two files to run:

  • The simplified gff file that was used as an input for a McScanX query.
  • The collinearity file generated as an output by McScanX for the same input query.
  • Optional track file in bedgraph format to annotate the generated charts.

SynVisio offers different types of visualizations such as Linear Parallel plots, Hive plots, Stacked Parallel Plots and Dot plots. Users can configure the type of plots required and then choose the source and the target chromosomes that need to be mapped. Users also have option to download the generated visualizations in publication ready SVG or PNG formats.

Address of the bookmark: https://synvisio.github.io/#/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/33693/circleator Sun, 25 Jun 2017 18:04:32 -0500 https://bioinformaticsonline.com/bookmarks/view/33693/circleator <![CDATA[Circleator]]> The Charm City Circleator--or Circleator for short--is a Perl-based visualization tool developed at the Institute for Genome Sciences in the University of Maryland's School of Medicine. Circleator produces circular plots of genome-associated data, like this one:

Sample Circleator image

Common uses of the tool include:

  • Displaying the sequence and/or genes in a GenBank flat file.
  • Highlighting differences and/or similarities in gene content between related organisms.
  • Comparing SNPs and indels between closely-related strains or serovars.
  • Comparing gene expression values across multiple samples or timepoints.
  • Visualizing coverage plots of RNA-Seq read alignments.

Key Features

Circleator...

  • Builds on BioPerl and the input file formats that it supports, including:
  • Accepts a number of other commonly-used datatypes and file formats:
    • BSR and TRF output, SAM/BAM files, VCF-encoded SNPs, tab-delimited files
  • Outputs publication-ready figures in the SVG (Scalable Vector Graphics) format.
  • Requires only a single configuration file whose layout mirrors that of the figure itself.
    • Predefined configuration files and "track" types are supplied for common datasets.
    • Advanced features allow limited analyses to be performed as a figure is drawn.
  • Includes an extensive set of regression tests.
  • Offers a prototype web-based GUI (under the "Ringmaster" project.)

https://github.com/jonathancrabtree/Circleator

Address of the bookmark: https://github.com/jonathancrabtree/Circleator

]]> Jit https://bioinformaticsonline.com/bookmarks/view/35135/alitv%E2%80%94interactive-visualization-of-whole-genome-comparisons Wed, 10 Jan 2018 07:08:17 -0600 https://bioinformaticsonline.com/bookmarks/view/35135/alitv%E2%80%94interactive-visualization-of-whole-genome-comparisons <![CDATA[AliTV—interactive visualization of whole genome comparisons]]> AliTV, which provides interactive visualization of whole genome alignments. AliTV reads multiple whole genome alignments or automatically generates alignments from the provided data. Optional feature annotations and phylo- genetic information are supported. The user-friendly, web-browser based and highly customizable interface allows rapid exploration and manipulation of the visualized data as well as the export of publication-ready high-quality figures. AliTV is freely available at https://github.com/AliTVTeam/AliTV

https://alitvteam.github.io/AliTV/

Address of the bookmark: https://github.com/AliTVTeam/AliTV

]]> Jit https://bioinformaticsonline.com/blog/view/37049/chromomap-an-r-package-for-interactive-visualization-and-mapping-of-human-chromosomes Mon, 25 Jun 2018 17:22:24 -0500 https://bioinformaticsonline.com/blog/view/37049/chromomap-an-r-package-for-interactive-visualization-and-mapping-of-human-chromosomes <![CDATA[chromoMap-An R package for Interactive visualization and mapping of human chromosomes]]> chromoMap is an R package that provides interactive, configurable and elegant graphics visualization of the human chromosomes allowing users to map chromosome elements (like genes, SNPs etc.) on the chromosome plot. It introduces a special plot viz. the "chromosome heatmap" that, in addition to mapping elements, can visualize the data associated with chromosome elements (like gene expression) in the form of heat colors which can be highly advantageous in the scientific interpretations and research work. Because of the enormous size of the chromosomes, it is impractical to visualize each element on the same plot. But chromoMap plots provide a magnified view for each of chromosome location to render additional information and visualization specific for that location. You can map thousands of genes and can view all mappings easily. Users can investigate the detailed information about the mappings (like gene names or total genes mapped on a location) or can view the magnified single or double stranded view of the chromosome at a location showing each mapped element in sequential order (You will see in the demos below). Not ony that, the plots can be saved as HTML documents that can be customized and shared easily. In addition, you can include them in R Markdown or in R Shiny applications.

https://cran.r-project.org/web/packages/chromoMap/index.html

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/37529/bokeh-an-interactive-visualization-library-that-targets-modern-web-browsers-for-presentation Fri, 10 Aug 2018 18:43:08 -0500 https://bioinformaticsonline.com/bookmarks/view/37529/bokeh-an-interactive-visualization-library-that-targets-modern-web-browsers-for-presentation <![CDATA[Bokeh: An interactive visualization library that targets modern web browsers for presentation]]> Bokeh is an interactive visualization library that targets modern web browsers for presentation. Its goal is to provide elegant, concise construction of versatile graphics, and to extend this capability with high-performance interactivity over very large or streaming datasets. Bokeh can help anyone who would like to quickly and easily create interactive plots, dashboards, and data applications.

To get started using Bokeh to make your visualizations, see the User Guide.

To see examples of how you might use Bokeh with your own data, check out the Gallery.

A complete API reference of Bokeh is at Reference Guide.

If you are interested in contributing to Bokeh, or extending the library, see the Developer Guide.

Address of the bookmark: https://bokeh.pydata.org/en/latest/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/40298/environment-for-tree-exploration-ete-is-a-python-programming-toolkit-that-assists-in-the-recontruction-manipulation-analysis-and-visualization-of-phylogenetic-trees Wed, 27 Nov 2019 05:32:33 -0600 https://bioinformaticsonline.com/bookmarks/view/40298/environment-for-tree-exploration-ete-is-a-python-programming-toolkit-that-assists-in-the-recontruction-manipulation-analysis-and-visualization-of-phylogenetic-trees <![CDATA[Environment for Tree Exploration (ETE) is a Python programming toolkit that assists in the recontruction, manipulation, analysis and visualization of phylogenetic trees]]> The Environment for Tree Exploration (ETE) is a Python programming toolkit that assists in the recontruction, manipulation, analysis and visualization of phylogenetic trees (although clustering trees or any other tree-like data structure are also supported).

Other tools

https://github.com/shenwei356/taxonkit

 

Address of the bookmark: https://pypi.org/project/ete3/3.1.1/

]]> Rahul Nayak https://bioinformaticsonline.com/bookmarks/view/43614/mitoz-a-toolkit-for-animal-mitochondrial-genome-assembly-annotation-and-visualization Tue, 30 Nov 2021 23:23:57 -0600 https://bioinformaticsonline.com/bookmarks/view/43614/mitoz-a-toolkit-for-animal-mitochondrial-genome-assembly-annotation-and-visualization <![CDATA[MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization]]> MitoZ, consisting of independent modules of de novo assembly, findMitoScaf (find Mitochondrial Scaffolds), annotation and visualization, that can generate mitogenome assembly together with annotation and visualization results from HTS raw reads.

https://academic.oup.com/nar/article/47/11/e63/5377471

Address of the bookmark: https://github.com/linzhi2013/MitoZ

]]> Neel https://bioinformaticsonline.com/bookmarks/view/44414/reconplot-an-r-package-for-the-visualization-and-interpretation-of-genomic-rearrangements Thu, 14 Dec 2023 12:33:19 -0600 https://bioinformaticsonline.com/bookmarks/view/44414/reconplot-an-r-package-for-the-visualization-and-interpretation-of-genomic-rearrangements <![CDATA[ReConPlot: an R package for the visualization and interpretation of genomic rearrangements]]> ReConPlot (REarrangement and COpy Number PLOT), an R package that provides functionalities for the joint visualization of SCNAs and SVs across one or multiple chromosomes. ReConPlot is based on the popular ggplot2 package, thus allowing customization of plots and the generation of publication-quality figures with minimal effort.

Address of the bookmark: https://academic.oup.com/bioinformatics/article/39/12/btad719/7460198?login=false

]]> LEGE