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GUANGCHUANGYU.GITHUB.IO

Guangchuang YU

PhD student

http://guangchuangyu.github.io/

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Guangchuang YU | guangchuangyu.github.io Reviews

https://guangchuangyu.github.io

PhD student

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1

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters | Guangchuang YU

http://guangchuangyu.github.io/publication/clusterProfiler

ClusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters. LG Wang, Y Han, QY He. OMICS: A Journal of Integrative Biology. Functional similarity analysis of human virus-encoded miRNAs. LXtoo: an integrated live Linux distribution for the bioinformatics community →. 2016 Guangchuang YU · Powered by the Academic theme.

2

Guangchuang Yu

http://guangchuangyu.github.io/cn

Mar 9, 2017 - 1 minute read - R. BED的全称是Browser Extensible Data,顾名思义是为genome browser设计的,大名鼎鼎的bedtools可不是什么 床上用品。 1 chrom - 染色体名字. 2 chromStart - 染色体起始位点. 3 chromEnd - 染色体终止位点. 很多分析软件都忽略 了这一点,会有一个碱基的位移,据我所知Homer和ChIPseeker没有这个问题,而像peakAnalyzer, ChIPpeakAnno等都有位移的问题。 4 name - 名字. 5 score - 分值(0-1000), 用于genome browser展示时上色。 6 strand - 正负链,对于ChIPseq数据来说, 一般. 7 thickStart - 画矩形的起点. 8 thickEnd - 画矩形的终点. 9 itemRgb - RGB值. 10 blockCount - 子元件 比如外显子 的数目. 11 blockSizes - 子元件的大小. 12 blockStarts - 子元件的起始位点.

3

ReactomePA

http://guangchuangyu.github.io/ReactomePA

ReactomePA: Reactome Pathway Analysis. Projects that depend on ReactomePA. ReactomePA: Reactome Pathway Analysis. 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. Is released within the Bioconductor. Project and the source code is hosted in. Guangchuang Yu, School of Public Health, The University of Hong Kong. Please cite the following article when using. For us...

4

ggtree for visualization and annotation of phylogenetic trees

http://guangchuangyu.github.io/presentation/2016-ggtree-chinar

Ggtree for visualization and annotation of phylogenetic trees. Ggtree for visualization and annotation of phylogenetic trees. What is a phylogenetic tree? A model of evolutionary history. Understanding life through time. Over long periods of past time. The connections between all groups of organisms as understood by ancestor-descendant. A phylogenetic tree is one possible. Representation of the relationships. Models are approximations or simplications of real-world systems. Phylogenetic tree file formats.

5

ggtree

http://guangchuangyu.github.io/ggtree

Getting tree into R. Tree visualization and annotation. Projects that depend on ggtree. Package. It based on grammar of graphics and takes all the good parts of. Is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree. Is released within the Bioconductor. Project and the source code is hosted on. Guangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The University of Hong Kong. Please cite the following article when using. Find out more on. Helper func...

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Guangchuang YU

The University of Hong Kong. I am Guangchuang YU. A PhD candidate studying evolution of influenza A virus at The University of Hong Kong. PhD in Evolution Study of Influenza A Virus, 2017. The University of Hong Kong. Master in Biochemistry and Molecular Biology, 2009. BSc in Biotechnology, 2005. South China Agricultural University. Ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Convert graphic object to tree object using treeio.

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