Search Results - "Yu, Guangchuang"

Gene Ontology Semantic Similarity Analysis Using GOSemSim by Yu, Guangchuang

“…The GOSemSim package, an R-based tool within the Bioconductor project, offers several methods based on information content and graph structure for measuring…”
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ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization by Yu, Guangchuang, Wang, Li-Gen, He, Qing-Yu

“…ChIPseeker is an R package for annotating ChIP-seq data analysis. It supports annotating ChIP peaks and provides functions to visualize ChIP peaks coverage…”
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ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization by Yu, Guangchuang, He, Qing-Yu

“…Reactome is a manually curated pathway annotation database for unveiling high-order biological pathways from high-throughput data. ReactomePA is an…”
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Thirteen years of clusterProfiler by Yu, Guangchuang

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Two Methods for Mapping and Visualizing Associated Data on Phylogeny Using Ggtree by Yu, Guangchuang, Lam, Tommy Tsan-Yuk, Zhu, Huachen, Guan, Yi

“…Ggtree is a comprehensive R package for visualizing and annotating phylogenetic trees with associated data. It can also map and visualize associated external…”
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ggVennDiagram: An Intuitive, Easy-to-Use, and Highly Customizable R Package to Generate Venn Diagram by Gao, Chun-Hui, Yu, Guangchuang, Cai, Peng

“…Venn diagrams are widely used diagrams to show the set relationships in biomedical studies. In this study, we developed ggVennDiagram, an R package that could…”
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DOSE: an R/Bioconductor package for disease ontology semantic and enrichment analysis by Yu, Guangchuang, Wang, Li-Gen, Yan, Guang-Rong, He, Qing-Yu

“…Disease ontology (DO) annotates human genes in the context of disease. DO is important annotation in translating molecular findings from high-throughput data…”
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Use ggbreak to Effectively Utilize Plotting Space to Deal With Large Datasets and Outliers by Xu, Shuangbin, Chen, Meijun, Feng, Tingze, Zhan, Li, Zhou, Lang, Yu, Guangchuang

“…With the rapid increase of large-scale datasets, biomedical data visualization is facing challenges. The data may be large, have different orders of magnitude,…”
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IOBR: Multi-Omics Immuno-Oncology Biological Research to Decode Tumor Microenvironment and Signatures by Zeng, Dongqiang, Ye, Zilan, Shen, Rongfang, Yu, Guangchuang, Wu, Jiani, Xiong, Yi, Zhou, Rui, Qiu, Wenjun, Huang, Na, Sun, Li, Li, Xuejun, Bin, Jianping, Liao, Yulin, Shi, Min, Liao, Wangjun

“…Recent advances in next-generation sequencing (NGS) technologies have triggered the rapid accumulation of publicly available multi-omics datasets. The…”
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clusterProfiler 4.0: A universal enrichment tool for interpreting omics data by Wu, Tianzhi, Hu, Erqiang, Xu, Shuangbin, Chen, Meijun, Guo, Pingfan, Dai, Zehan, Feng, Tingze, Zhou, Lang, Tang, Wenli, Zhan, Li, Fu, Xiaocong, Liu, Shanshan, Bo, Xiaochen, Yu, Guangchuang

“…Functional enrichment analysis is pivotal for interpreting high-throughput omics data in life science. It is crucial for this type of tool to use the latest…”
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CBNplot: Bayesian network plots for enrichment analysis by Sato, Noriaki, Tamada, Yoshinori, Yu, Guangchuang, Okuno, Yasushi

“…Abstract Summary When investigating gene expression profiles, determining important directed edges between genes can provide valuable insights in addition to…”
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RIdeogram : drawing SVG graphics to visualize and map genome-wide data on the idiograms by Hao, Zhaodong, Lv, Dekang, Ge, Ying, Shi, Jisen, Weijers, Dolf, Yu, Guangchuang, Chen, Jinhui

“…Owing to the rapid advances in DNA sequencing technologies, whole genome from more and more species are becoming available at increasing pace. For whole-genome…”
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GOSemSim: an R package for measuring semantic similarity among GO terms and gene products by Yu, Guangchuang, Li, Fei, Qin, Yide, Bo, Xiaochen, Wu, Yibo, Wang, Shengqi

“…The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became…”
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clusterProfiler: an R package for comparing biological themes among gene clusters by Yu, Guangchuang, Wang, Li-Gen, Han, Yanyan, He, Qing-Yu

“…Increasing quantitative data generated from transcriptomics and proteomics require integrative strategies for analysis. Here, we present an R package,…”
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ggmsa: a visual exploration tool for multiple sequence alignment and associated data by Zhou, Lang, Feng, Tingze, Xu, Shuangbin, Gao, Fangluan, Lam, Tommy T, Wang, Qianwen, Wu, Tianzhi, Huang, Huina, Zhan, Li, Li, Lin, Guan, Yi, Dai, Zehan, Yu, Guangchuang

“…Abstract The identification of the conserved and variable regions in the multiple sequence alignment (MSA) is critical to accelerating the process of…”
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Ggtree: A serialized data object for visualization of a phylogenetic tree and annotation data by Xu, Shuangbin, Li, Lin, Luo, Xiao, Chen, Meijun, Tang, Wenli, Zhan, Li, Dai, Zehan, Lam, Tommy T., Guan, Yi, Yu, Guangchuang

“…While phylogenetic trees and associated data have been getting easier to generate, it has been difficult to reuse, combine, and synthesize the information they…”
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Reducing language barriers, promoting information absorption, and communication using fanyi by Wang, Difei, Chen, Guannan, Li, Lin, Wen, Shaodi, Xie, Zijing, Luo, Xiao, Zhan, Li, Xu, Shuangbin, Li, Junrui, Wang, Rui, Wang, Qianwen, Yu, Guangchuang

“…Interpreting genes of interest is essential for identifying molecular mechanisms, but acquiring such information typically involves tedious manual retrieval…”
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MicrobiotaProcess: A comprehensive R package for deep mining microbiome by Xu, Shuangbin, Zhan, Li, Tang, Wenli, Wang, Qianwen, Dai, Zehan, Zhou, Lang, Feng, Tingze, Chen, Meijun, Wu, Tianzhi, Hu, Erqiang, Yu, Guangchuang

“…The data output from microbiome research is growing at an accelerating rate, yet mining the data quickly and efficiently remains difficult. There is still a…”
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nCov2019: an R package for studying the COVID-19 coronavirus pandemic by Wu, Tianzhi, Hu, Erqiang, Ge, Xijin, Yu, Guangchuang

“…The global spreading of the COVID-19 coronavirus is still a serious public health challenge. Although there are a large number of public resources that provide…”
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Gut microbiome and metabolome to discover pathogenic bacteria and probiotics in ankylosing spondylitis by Lai, Yupeng, Tang, Wenli, Luo, Xiao, Zheng, Huihui, Zhang, Yanpeng, Wang, Meiying, Yu, Guangchuang, Yang, Min

“…Previous research has partially revealed distinct gut microbiota in ankylosing spondylitis (AS). In this study, we performed non-targeted fecal metabolomics in…”
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