BOL: Related items

fineSTRUCTURE v2 & GLOBETROTTER

Shruti Paniwala — Mon, 13 Feb 2017 08:40:23 -0600

Software available at this site

FineSTRUCTURE version 2, a pipeline for running ChromoPainter and FineSTRUCTURE for population inference. A GUI is available for interpretation. Download from the Downloads page.
FineSTRUCTURE R scripts, a facility for exploring the results when the GUI is unavailable.
GLOBETROTTER, the admixture dating method based on ChromoPainter. Download from the Downloads page.
AdmixturePainting, A set of R tools to inmterpret the results of ADMIXTURE and STRUCTURE-like mixture models.
RADpainter, finestructure and ChromoPainter for RAD tag data used for non-model organisms.
Scripts to perform many types of conversion. Included in the main software download from the Downloads page.

What this page is This page provides information about and downloads for methodology for Chromosome Painting. It is not a facility to analyse your genome. Sorry if you were misled by the punchy name!
About Chromosome Painting Painting is an efficient way of identifying important haplotype information from dense genotype data. It describes ancestry in an efficient way suitable for a range of further analyses, including population identification and admixture dating.

Address of the bookmark: http://paintmychromosomes.com/

Circular plots in R

Jit — Mon, 19 Jun 2017 06:20:27 -0500

Circular plots are useful to represent complicated informations. They are used in 2 specific cases: when you have long axis and numerous categories, and when you want to show relationships between elements. The circos gallery displays several examples of circular plots, what gives a nice overview of the possibilities. Circos is the most famous

tool to create circular plots. Thanks to Zuguang Gu, the Circlize library makes the circos functions available in R! It implements low-level graphic functions for adding common graphics in a circular layout. This page aims to learn you how to use the library, so I strongly advise to read the graphics in the proposed order!

http://www.r-graph-gallery.com/portfolio/circular-plot/

Address of the bookmark: http://www.r-graph-gallery.com/portfolio/circular-plot/

poRe: an R package for the visualization and analysis of nanopore sequencing data

Jit — Thu, 23 Nov 2017 09:55:57 -0600

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

dupRadar package

Jit — Sun, 04 Feb 2018 14:28:57 -0600

The dupRadar package gives an insight into the duplication problem by graphically relating the gene expression level and the duplication rate present on it. Thus, failed experiments can be easily identified at a glance

Address of the bookmark: https://bioconductor.org/packages/3.7/bioc/vignettes/dupRadar/inst/doc/dupRadar.html

ASAR: Advanced metagenomic Sequence Analysis in R

Jit — Mon, 09 Jul 2018 05:20:50 -0500

An interactive data analysis tool for selection, aggregation and visualization of metagenomic data is presented. Functional analysis with a SEED hierarchy and pathway diagram based on KEGG orthology based upon MG-RAST annotation results is available.

To read the manual, please click the link https://askarbek-orakov.github.io/ASAR/

Address of the bookmark: https://github.com/Askarbek-orakov/ASAR

MetaPlotR: a Perl/R pipeline for plotting metagenes of nucleotide modifications and other transcriptomic sites

Neel — Mon, 05 Nov 2018 08:12:45 -0600

An increasing number of studies are mapping protein binding and nucleotide modifications sites throughout the transcriptome. Often, these sites cluster in certain regions of the transcript, giving clues to their function. Hence, it is informative to summarize where in the transcript these sites occur. A metagene is a simple and effective tool for visualizing the distribution of sites along a simplified transcript model. In this work, we introduce MetaPlotR, a Perl/R pipeline for creating metagene plots.

Address of the bookmark: https://github.com/olarerin/metaPlotR

genoPlotR - plot gene and genome maps project!

Abhimanyu Singh — Wed, 12 Dec 2018 08:33:41 -0600

genoPlotR is a R package to produce reproducible, publication-grade graphics of gene and genome maps. It allows the user to read from usual format such as protein table files and blast results, as well as home-made tabular files.

Features

Linear representation of several segments of DNA
Comparisons represented by areas between the segments (like Artemis, for example)
Reads from common formats: Genbank, EMBL, blast, Mauve, and from user-generated tab files
Plot several subsegments of the same segment on the same line, separated by a //
Automatic or manual placement of the segments on the plot
Add annotations to all the lines
Create smart, automatic annotations for genomes, based on gene names
Add a user-generated tree
Add a global scale or a scale to each line
Use user-defined graphical functions to represent genes

Address of the bookmark: http://genoplotr.r-forge.r-project.org/

chromoMap-An R package for Interactive Visualization and Annotation of Chromosomes

Neel — Fri, 12 Apr 2019 05:30:41 -0500

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

alluvial diagram

Jit — Sat, 21 Sep 2019 07:31:08 -0500

Alluvial diagram is a variant of a Parallel Coordinates Plot (PCP) but for categorical variables. Variables are assigned to vertical axes that are parallel. Values are represented with blocks on each axis. Observations are represented with alluvia (sing. “alluvium”) spanning across all the axes.

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

EFS: an ensemble feature selection tool implemented as R-package and web-application

Jit — Tue, 28 Jan 2020 05:12:23 -0600

The software EFS (Ensemble Feature Selection) makes use of multiple feature selection methods and combines their normalized outputs to a quantitative ensemble importance. Currently, eight different feature selection methods have been integrated in EFS, which can be used separately or combined in an ensemble.

https://biodatamining.biomedcentral.com/articles/10.1186/s13040-017-0142-8

Address of the bookmark: http://efs.heiderlab.de/