<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/44414? https://bioinformaticsonline.com/bookmarks/view/38420/regioner-an-r-package-for-the-management-and-comparison-of-genomic-regions Tue, 11 Dec 2018 08:43:51 -0600 https://bioinformaticsonline.com/bookmarks/view/38420/regioner-an-r-package-for-the-management-and-comparison-of-genomic-regions <![CDATA[regioneR: an R package for the management and comparison of genomic regions]]> Regioner is an R package for the management and comparison of genomic regions. It offers a set of function for basic manipulation of region sets extending the functionality of GenomicRanges and a powerful and customizable permutation test framework. With it, it's possible to study the association of a set of regions with other sets of regions, functions defined over the genome or essentially any user defined function.

http://gattaca.imppc.org/regioner/

Address of the bookmark: http://gattaca.imppc.org/regioner/

]]> Jit 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/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/34396/pore-an-r-package-for-the-visualization-and-analysis-of-nanopore-sequencing-data Thu, 23 Nov 2017 09:55:57 -0600 https://bioinformaticsonline.com/bookmarks/view/34396/pore-an-r-package-for-the-visualization-and-analysis-of-nanopore-sequencing-data <![CDATA[poRe: an R package for the visualization and analysis of nanopore sequencing data]]> Motivation: The Oxford Nanopore MinION device represents a unique sequencing technology. As a mobile sequencing device powered by the USB port of a laptop, the MinION has huge potential applications. To enable these applications, the bioinformatics community will need to design and build a suite of tools specifically for MinION data.

Results: Here we present poRe, a package for R that enables users to manipulate, organize, summarize and visualize MinION nanopore sequencing data. As a package for R, poRe has been tested on Windows, Linux and MacOSX. Crucially, the Windows version allows users to analyse MinION data on the Windows laptop attached to the device.

Availability and implementation: poRe is released as a package for R at http://sourceforge.net/projects/rpore/ . A tutorial and further information are available at https://sourceforge.net/p/rpore/wiki/Home/

Contact:mick.watson@roslin.ed.ac.uk

Address of the bookmark: https://academic.oup.com/bioinformatics/article/31/1/114/2365693

]]> 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/39244/chromomap-an-r-package-for-interactive-visualization-and-annotation-of-chromosomes Fri, 12 Apr 2019 05:30:41 -0500 https://bioinformaticsonline.com/bookmarks/view/39244/chromomap-an-r-package-for-interactive-visualization-and-annotation-of-chromosomes <![CDATA[chromoMap-An R package for Interactive Visualization and Annotation of Chromosomes]]> Provides interactive, configurable and elegant graphics visualization of the chromosomes or chromosome regions of any living organism 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. The package provide multiple features like visualizing multiple sets, chromosome heat-maps, group annotations, adding hyperlinks, and labelling. 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.

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

]]> Neel https://bioinformaticsonline.com/bookmarks/view/38804/grabb-selective-assembly-of-genomic-regions-a-new-niche-for-genomic-research Sat, 26 Jan 2019 18:58:16 -0600 https://bioinformaticsonline.com/bookmarks/view/38804/grabb-selective-assembly-of-genomic-regions-a-new-niche-for-genomic-research <![CDATA[GRAbB: Selective Assembly of Genomic Regions, a New Niche for Genomic Research]]> GRAbB is shown to be more efficient than MITObim in terms of speed, memory and disk usage. The other functionalities (handling multiple targets simultaneously and extracting homologous regions) of the new program are not matched by other programs. The program is available with explanatory documentation at https://github.com/b-brankovics/grabb. GRAbB has been tested on Ubuntu (12.04 and 14.04), Fedora (23), CentOS (7.1.1503) and Mac OS X (10.7). Furthermore, GRAbB is available as a docker repository: brankovics/grabb (https://hub.docker.com/r/brankovics/grabb/).

Address of the bookmark: https://github.com/b-brankovics/grabb

]]> Rahul Nayak https://bioinformaticsonline.com/news/view/19087/dcgor Sat, 08 Nov 2014 14:54:28 -0600 https://bioinformaticsonline.com/news/view/19087/dcgor <![CDATA[dcGOR]]> An R package for analysing ontologies and protein domain annotations has been published in PLoS Computational Biology (http://dx.doi.org/10.1371/journal.pcbi.1003929). The package is distributed as part of CRAN (http://cran.r-project.org/package=dcGOR), and also at GitHub for version control.

The dedicated website is available in http://supfam.org/dcGOR, from which several demos are also provided:

1. Analysing SCOP domains: http://supfam.org/dcGOR/demo-Fang.html

2. Analysing Pfam domains: http://supfam.org/dcGOR/demo-Basu.html

3. Analysing InterPro domains: http://supfam.org/dcGOR/demo-Customisation.html

 

]]> Martin Jones