<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/34396? https://bioinformaticsonline.com/bookmarks/view/37527/nanopack-visualizing-and-processing-long-read-sequencing-data Fri, 10 Aug 2018 18:41:34 -0500 https://bioinformaticsonline.com/bookmarks/view/37527/nanopack-visualizing-and-processing-long-read-sequencing-data <![CDATA[NanoPack: visualizing and processing long-read sequencing data]]> The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are compatible with Linux, Mac OS and the MS Windows 10 subsystem for Linux and are available as a graphical user interface, a web service at http://nanoplot.bioinf.be and command line tools.

 https://academic.oup.com/bioinformatics/article/34/15/2666/4934939

Address of the bookmark: https://github.com/wdecoster/nanoQC

]]> Jit 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/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/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 https://bioinformaticsonline.com/bookmarks/view/28855/vcfr Fri, 19 Aug 2016 07:38:24 -0500 https://bioinformaticsonline.com/bookmarks/view/28855/vcfr <![CDATA[vcfR]]> Most variant calling pipelines result in files containing large quantities of variant information. The variant call format (vcf) is an increasingly popular format for this data. The format of these files and their content is discussed in the vignette ‘vcf data.’ These files are typically intended to be post-processed (i.e., filtered) as an attempt to remove false positives or otherwise problematic sites. The R package vcfR provides tools to facilitate this filtering as well as to visualize the effects of choices made during this process.

Address of the bookmark: https://cran.r-project.org/web/packages/vcfR/vignettes/visualization_1.html

]]> Archana Malhotra https://bioinformaticsonline.com/bookmarks/view/27427/rcircos-an-r-package-for-circos-2d-track-plots Fri, 20 May 2016 11:01:13 -0500 https://bioinformaticsonline.com/bookmarks/view/27427/rcircos-an-r-package-for-circos-2d-track-plots <![CDATA[RCircos: an R package for Circos 2D track plots]]> RCircos package provides a simple and flexible way to make Circos 2D track plots with R and could be easily integrated into other R data processing and graphic manipulation pipelines for presenting large-scale multi-sample genomic research data. It can also serve as a base tool to generate complex Circos images.

More at https://bitbucket.org/henryhzhang/rcircos/src

Address of the bookmark: https://bitbucket.org/henryhzhang/rcircos/src

]]> Jit https://bioinformaticsonline.com/bookmarks/view/38646/visnetwork-an-r-package-for-network-visualization-using-visjs-javascript-library Wed, 09 Jan 2019 11:00:32 -0600 https://bioinformaticsonline.com/bookmarks/view/38646/visnetwork-an-r-package-for-network-visualization-using-visjs-javascript-library <![CDATA[visNetwork: an R package for network visualization, using vis.js javascript library]]>

visNetwork is an R package for network visualization, using vis.js javascript library (http://visjs.org/). All remarks and bugs are welcome on github : https://github.com/datastorm-open/visNetwork.

Features

Based on htmlwidgets, so :

  • compatible with shiny, R Markdown documents, and RStudio viewer

The package proposes all the features available in vis.js API, and even more with special features for R :

  • easy to use
  • custom shapes, styles, colors, sizes, …
  • works smooth on any modern browser for up to a few thousand nodes and edges
  • interactivity controls (highlight, collapsed nodes, selection, zoom, physics, movement of nodes, tooltip, events, …)
  • visualize rpart tree

Address of the bookmark: https://datastorm-open.github.io/visNetwork/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/40964/panev-an-r-package-for-a-pathway-based-network-visualization Sun, 09 Feb 2020 12:41:52 -0600 https://bioinformaticsonline.com/bookmarks/view/40964/panev-an-r-package-for-a-pathway-based-network-visualization <![CDATA[PANEV: an R package for a pathway-based network visualization]]> PANEV (PAthway NEtwork Visualizer) is an R package set for gene/pathway-based network visualization. Based on information available on KEGG, it visualizes genes within a network of multiple levels (from 1 to n) of interconnected upstream and downstream pathways. The network graph visualization helps to interpret functional profiles of a cluster of genes.

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3371-7

Address of the bookmark: https://github.com/vpalombo/PANEV

]]> Jit https://bioinformaticsonline.com/bookmarks/view/35635/ete-3-reconstruction-analysis-and-visualization-of-phylogenomic-data Mon, 19 Feb 2018 06:46:15 -0600 https://bioinformaticsonline.com/bookmarks/view/35635/ete-3-reconstruction-analysis-and-visualization-of-phylogenomic-data <![CDATA[ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data]]> ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics.

The new features include

(i) building gene-based and supermatrix-based phylogenies using a single command,

(ii) testing and visualizing evolutionary models,

(iii) calculating distances between trees of different size or including duplications, and

(iv) providing seamless integration with the NCBI taxonomy database.

ETE is freely available at http://etetoolkit.org

Address of the bookmark: http://etetoolkit.org

]]> Jit https://bioinformaticsonline.com/bookmarks/view/39875/lrsday-long-read-sequencing-data-analysis-for-yeasts Mon, 26 Aug 2019 18:07:33 -0500 https://bioinformaticsonline.com/bookmarks/view/39875/lrsday-long-read-sequencing-data-analysis-for-yeasts <![CDATA[LRSDAY: Long-read Sequencing Data Analysis for Yeasts]]> Long-read sequencing technologies have become increasingly popular in genome projects due to their strengths in resolving complex genomic regions. As a leading model organism with small genome size and great biotechnological importance, the budding yeast, Saccharomyces cerevisiae, has many isolates currently being sequenced with long reads. 

Address of the bookmark: https://github.com/yjx1217/LRSDAY

]]> Poonam Mahapatra