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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).

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.

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Version

Install

install.packages('RIdeogram')

Monthly Downloads

465

Version

0.2.0

License

Artistic-2.0

Maintainer

Zhaodong Hao

Last Published

November 8th, 2019

Functions in RIdeogram (0.2.0)

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