Guangchuang Yu

Guangchuang Yu

19 packages on CRAN

7 packages on Bioconductor

badger

cran
99.99th

Percentile

Query information and generate badge for using in README and GitHub Pages.

base2grob

cran
99.99th

Percentile

Convert base plot function call (using expression or formula) to 'grob' object that compatible to the 'grid' ecosystem. With this package, we are able to e.g. using 'cowplot' to align base plots with 'ggplot' objects and using 'ggsave' to export base plot to file.

dlstats

cran
99.99th

Percentile

Monthly download stats of 'CRAN' and 'Bioconductor' packages. Download stats of 'CRAN' packages is from the 'RStudio' 'CRAN mirror', see <http://cranlogs.r-pkg.org>. 'Bioconductor' package download stats is at <https://bioconductor.org/packages/stats/>.

emojifont

cran
99.99th

Percentile

An implementation of using emoji and fontawesome for using in both base and 'ggplot2' graphics.

ggimage

cran
99.99th

Percentile

Supports image files and graphic objects to be visualized in 'ggplot2' graphic system.

ggmsa

cran
99.99th

Percentile

Supports visualizing multiple sequence alignment of DNA and protein sequences using 'ggplot2'. It supports a number of colour schemes, including Chemistry, Clustal, Shapely, Taylor and Zappo. Multiple sequence alignment can easily be combined with other 'ggplot2' plots, such as aligning a phylogenetic tree produced by 'ggtree' with multiple sequence alignment.

ggplotify

cran
99.99th

Percentile

Convert plot function call (using expression or formula) to 'grob' or 'ggplot' object that compatible to the 'grid' and 'ggplot2' ecosystem. With this package, we are able to e.g. using 'cowplot' to align plots produced by 'base' graphics, 'grid', 'lattice', 'vcd' etc. by converting them to 'ggplot' objects.

hexSticker

cran
99.99th

Percentile

Helper functions for creating reproducible hexagon sticker purely in R.

ChIPseeker

bioconductor
99.99th

Percentile

This package implements functions to retrieve the nearest genes around the peak, annotate genomic region of the peak, statstical methods for estimate the significance of overlap among ChIP peak data sets, and incorporate GEO database for user to compare the own dataset with those deposited in database. The comparison can be used to infer cooperative regulation and thus can be used to generate hypotheses. Several visualization functions are implemented to summarize the coverage of the peak experiment, average profile and heatmap of peaks binding to TSS regions, genomic annotation, distance to TSS, and overlap of peaks or genes.

clusterProfiler

bioconductor
99.99th

Percentile

This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene and gene clusters.

DOSE

bioconductor
99.99th

Percentile

This package implements five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively for measuring semantic similarities among DO terms and gene products. Enrichment analyses including hypergeometric model and gene set enrichment analysis are also implemented for discovering disease associations of high-throughput biological data.

ggtree

bioconductor
99.99th

Percentile

ggtree extends the ggplot2 plotting system which implemented the grammar of graphics. ggtree is designed for visualizing phylogenetic tree and different types of associated annotation data.

GOSemSim

bioconductor
99.99th

Percentile

Implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively for estimating GO semantic similarities. Support many species, including Anopheles, Arabidopsis, Bovine, Canine, Chicken, Chimp, Coelicolor, E coli strain K12 and Sakai, Fly, Gondii, Human, Malaria, Mouse, Pig, Rhesus, Rat, Worm, Xenopus, Yeast, and Zebrafish.

meme

cran
99.99th

Percentile

The word 'Meme' was originated from the book, 'The Selfish Gene', authored by Richard Dawkins (1976). It is a unit of culture that is passed from one generation to another and correlates to the gene, the unit of physical heredity. The internet memes are captioned photos that are intended to be funny, ridiculous. Memes behave like infectious viruses and travel from person to person quickly through social media. The 'meme' package allows users to make custom memes.

rvcheck

cran
99.99th

Percentile

Check latest release version of R and R package (both in 'CRAN', 'Bioconductor' or 'Github').

scatterpie

cran
99.99th

Percentile

Creates scatterpie plots, especially useful for plotting pies on a map.

scholar

cran
99.99th

Percentile

Provides functions to extract citation data from Google Scholar. Convenience functions are also provided for comparing multiple scholars and predicting future h-index values.

shadowtext

cran
99.99th

Percentile

Implement shadowtextGrob() for 'grid' and geom_shadowtext() layer for 'ggplot2'. These functions create/draw text grob with background shadow.

ReactomePA

bioconductor
99.99th

Percentile

This package provides functions for pathway analysis based on REACTOME pathway database. It implements enrichment analysis, gene set enrichment analysis and several functions for visualization.

tidytree

cran
99.99th

Percentile

Phylogenetic tree generally contains multiple components including node, edge, branch and associated data. 'tidytree' provides an approach to convert tree object to tidy data frame as well as provides tidy interfaces to manipulate tree data.

99.99th

Percentile

Plot, draw regression line and confidence interval, and show regression equation, R-square and P-value, as simple as possible, by using different models ("line2P", "line3P", "log2P", "exp2P", "exp3P", "power2P", "power3P") built in the 'trendline()' function.

cowsay

cran
99.99th

Percentile

Allows printing of character strings as messages/warnings/etc. with ASCII animals, including cats, cows, frogs, chickens, ghosts, and more.

99.99th

Percentile

Easy-to-use functions to generate 2-4 sets Venn plot in publication quality. 'ggVennDiagram' is the first software that can automatically fill different colors to each part of a Venn diagram.

kableExtra

cran
99.99th

Percentile

Build complex HTML or 'LaTeX' tables using 'kable()' from 'knitr' and the piping syntax from 'magrittr'. Function 'kable()' is a light weight table generator coming from 'knitr'. This package simplifies the way to manipulate the HTML or 'LaTeX' codes generated by 'kable()' and allows users to construct complex tables and customize styles using a readable syntax.

RIdeogram

cran
99.99th

Percentile

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 in idiograms with no restriction of species.

MSnbase

bioconductor
99.99th

Percentile

Basic plotting, data manipulation and processing of MS-based Proteomics data.