<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/44541?offset=220 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/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/38541/geneoverlap-an-r-package-to-test-and-visualize-gene-overlaps Thu, 27 Dec 2018 19:45:52 -0600 https://bioinformaticsonline.com/bookmarks/view/38541/geneoverlap-an-r-package-to-test-and-visualize-gene-overlaps <![CDATA[GeneOverlap: An R package to test and visualize gene overlaps]]> Overlapping gene lists can reveal biological meanings and may lead to novel hypotheses. For example, histone modification is an important cellular mechanism that can pack and re-pack chromatin. By making the chromatin structure more dense or loose, the gene expression can be turned on or off. Tri-methylation on lysine 4 of histone H3 (H3K4me3) is associated with gene activation and its genome-wide enrichment can be mapped by using ChIP-seq experiments. Because of its activating role, if we overlap the genes that are bound by H3K4me3 with the genes that are highly expressed, we should expect a positive association. Similary, we can perform such kind of overlapping between the gene lists of different histone modifications with that of various expression groups and establish each histone modification’s role in gene regulation.

Address of the bookmark: https://bioconductor.org/packages/release/bioc/vignettes/GeneOverlap/inst/doc/GeneOverlap.pdf

]]> Jit https://bioinformaticsonline.com/bookmarks/view/39917/chromomap-an-r-package-for-interactive-visualization-and-annotation-of-chromosomes Sat, 07 Sep 2019 10:45:31 -0500 https://bioinformaticsonline.com/bookmarks/view/39917/chromomap-an-r-package-for-interactive-visualization-and-annotation-of-chromosomes <![CDATA[chromoMap-An R package for Interactive Visualization and Annotation of Chromosomes]]> chromoMap provides interactive, configurable and elegant graphics visualization of chromosomes or chromosomal regions allowing users to map chromosome elements (like genes,SNPs etc.) on the chromosome plot.Each chromosome is composed of loci(representing a specific range determined based on chromosome length) that, on hover, shows details about the annotations in that locus range. The plots can be saved as HTML documents that can be shared easily. In addition, you can include them in R Markdown or in R Shiny applications.

Some of the prominent features of the package are:

  • visualizing polyploidy simultaneously on the same plot.
  • annotating groups of elements as distinct colors.
  • creating chromosome heatmaps.
  • adjusting chromosome range or visualizing chromosome regions such as genes
  • adding labels to the plot
  • adding hyperlinks to each element

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

]]> Jit https://bioinformaticsonline.com/news/view/40085/github-replacement Thu, 26 Sep 2019 03:42:39 -0500 https://bioinformaticsonline.com/news/view/40085/github-replacement <![CDATA[Github replacement !]]> For a number of reasons researchers have been trying out GitLab as a replacement for for both GitHub and various continuous integration systems, and have been exploring configurations useful for model-fitting pipelines. Researchers turned one of these into an example repository that shows how to use GitLab together with the Rocker Docker images and the drake build system to reproducibly run a project pipeline, using the cacheing functionality across all three tools to make things reasonably speedy and enable both local and remote builds.

Check it out at https://gitlab.com/ecohealthalliance/drake-gitlab-docker-example.

]]> Rahul Nayak 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/41272/rainbowr-reliable-association-inference-by-optimizing-weights-with-r-r-package-for-snp-set-gwas-and-multi-kernel-mixed-model Fri, 28 Feb 2020 23:27:37 -0600 https://bioinformaticsonline.com/bookmarks/view/41272/rainbowr-reliable-association-inference-by-optimizing-weights-with-r-r-package-for-snp-set-gwas-and-multi-kernel-mixed-model <![CDATA[RAINBOWR: Reliable Association INference By Optimizing Weights with R (R package for SNP-set GWAS and multi-kernel mixed model)]]> RAINBOWR(Reliable Association INference By Optimizing Weights with R) is a package to perform several types of GWAS as follows.

  • Single-SNP GWAS with RGWAS.normal function
  • SNP-set (or gene set) GWAS with RGWAS.multisnp function (which tests multiple SNPs at the same time)
  • Check epistatic (SNP-set x SNP-set interaction) effects with RGWAS.epistasis (very slow and less reliable)

https://github.com/KosukeHamazaki/RAINBOWR

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007663

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

Address of the bookmark: https://github.com/KosukeHamazaki/RAINBOWR

]]> Surabhi Chaudhary https://bioinformaticsonline.com/bookmarks/view/42313/crbhits-from-conditional-reciprocal-best-hits-to-codon-alignments-and-kaks-in-r Wed, 11 Nov 2020 23:06:03 -0600 https://bioinformaticsonline.com/bookmarks/view/42313/crbhits-from-conditional-reciprocal-best-hits-to-codon-alignments-and-kaks-in-r <![CDATA[CRBHits: From Conditional Reciprocal Best Hits to Codon Alignments and Ka/Ks in R]]> CRBHits is a coding sequence (CDS) analysis pipeline in R (R Core Team, 2019). It reimplements the Conditional Reciprocal Best Hit (CRBH) algorithm crb-blast and covers all necessary steps from sequence similarity searches, codon alignments to Ka/Ks calculations and synteny. The new R package targets ecology, population and evolutionary biologists working in the field of comparative genomics.

Address of the bookmark: https://gitlab.gwdg.de/mpievolbio-it/crbhits

]]> Shruti Paniwala https://bioinformaticsonline.com/bookmarks/view/44362/biostats-book Mon, 14 Aug 2023 03:11:39 -0500 https://bioinformaticsonline.com/bookmarks/view/44362/biostats-book <![CDATA[Biostats book !]]> https://practical-stats-med-r.netlify.app/

Address of the bookmark: https://practical-stats-med-r.netlify.app/

]]> Abhi https://bioinformaticsonline.com/bookmarks/view/44663/svbyeye-r-package-to-visualize-alignments-between-two-or-multiple-dna-sequences Tue, 17 Sep 2024 02:34:57 -0500 https://bioinformaticsonline.com/bookmarks/view/44663/svbyeye-r-package-to-visualize-alignments-between-two-or-multiple-dna-sequences <![CDATA[SVbyEye: R Package to visualize alignments between two or multiple DNA sequences]]> R Package to visualize alignments between two or multiple DNA sequences including
a number of functionalities to facilitate processing of alignments in PAF format.

SVbyEye, an open-source R package to visualize and annotate sequence-to-sequence alignments along with various functionalities to process alignments in PAF format. The tool facilitates the characterization of complex SVs in the context of sequence homology helping resolve the mechanisms underlying their formation. Availability and implementation SVbyEye is available at https://github.com/daewoooo/SVbyEye.

Author: David Porubsky

Address of the bookmark: https://github.com/daewoooo/SVbyEye

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