RIdeogram v0.2.0

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Drawing SVG Graphics to Visualize and Map Genome-Wide Data on Idiograms

For whole-genome analysis, idiograms are virtually the most intuitive and effective way to map and visualize the genome-wide information. RIdeogram was developed to visualize and map whole-genome data on idiograms with no restriction of species.

Readme

RIdeogram: Drawing SVG Graphics to Visualize and Map Genome-Wide Data on Idiograms

RIdeogram is a R package to draw SVG graphics to visualize and map genome-wide data on idiograms (Scalable Vector Graphics http://tutorials.jenkov.com/svg/index.html).

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Installation

To install package from Github, you need to install the devtools package first

install.packages("devtools")
library(devtools)

Then, you can install the package RIdeogram

devtools::install_github('TickingClock1992/RIdeogram')

To install the package RIdeogram from CRAN

install.package("RIdeogram")

Citation

Zhaodong Hao, Dekang Lv, Ying Ge, Jisen Shi, Dolf Weijers, Guangchuang Yu, and Jinhui Chen (2019). RIdeogram: Drawing SVG graphics to visualize and map genome-wide data on idiograms. R package version 0.2.0.

Usage

https://cran.r-project.org/web/packages/RIdeogram/vignettes/RIdeogram.html

Maintainer

Zhaodong Hao haozd1992@163.com
Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education of China
College of Forestry, Nanjing Forestry University
Nanjing 210037, China

https://github.com/TickingClock1992

THANKS

Welcome to any suggestions and discussions.

Functions in RIdeogram

Name Description
Pi_for_CE_and_CW Pi of two Liriodendron groups
karyotype_dual_comparison Karyotype for two genome comparison
Random_RNAs_500 500 RNAs' position
karyotype_ternary_comparison Karyotype for three genome comparison
synteny_dual_comparison Synteny for two genome comparison
liriodendron_karyotype Karyotype information of the Liriodendron genome
LTR_density LTR distribution across the human genome
Pi_for_CE Pi of one Liriodendron group
Fst_between_CE_and_CW Fst between two Liriodendron groups
GFFex GFFex
synteny_ternary_comparison Synteny for three genome comparison
synteny_ternary_comparison_graident Synteny for three genome comparison with gradient fill
gene_density Gene distribution across the human genome
convertSVG convertSVG
ideogram ideogram
human_karyotype Karyotype information of the human genome
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Vignettes of RIdeogram

Name
figures/example1.png
figures/example10.png
figures/example11.png
figures/example12.png
figures/example13.png
figures/example14.png
figures/example15.png
figures/example16.png
figures/example17.png
figures/example2.png
figures/example3.png
figures/example4.png
figures/example5.png
figures/example6.png
figures/example7.png
figures/example8.png
figures/example9.png
RIdeogram.Rmd
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Details

Type Package
License Artistic-2.0
Encoding UTF-8
LazyData true
RoxygenNote 6.1.1
VignetteBuilder knitr
NeedsCompilation no
Packaged 2019-11-08 14:38:45 UTC; haozhaodong
Repository CRAN
Date/Publication 2019-11-08 15:00:02 UTC

Include our badge in your README

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