上面3个工具R包与网页版功能是一致的,但是在国内建议网页版,因为3个R包需要连接到外网,真的很慢~ PART 04 cluster profiler 最后就是Y叔开发的R包cluster profiler,至今被引用率2518次,也可以用来做如GO、KEGG、DO(Disease Ontology analysis)、Reactome pathway analysis以及GSEA富集分析等,就是昨天jimmy老师介绍的:...
同时也可以通过R包gprofiler2来实现 软件包安装 if(require(gprofiler2)) install.packages("gprofiler2") ## 载入需要的程辑包:gprofiler2 g:GOSt library(gprofiler2) gostres <- gost(query = c("X:1000:1000000", "rs17396340", "GO:0005005", "ENSG00000156103", "NLRP1"), organism = "hsapie...
转录组下游差异表达分析获取到很多基因,如何将这些基因归类,如何知道他们的功能,那就需要做功能富集分析,常用的有GO功能富集和KEGG通路富集分析,在R中使用tidyverse数据处理包和功能富集包clusterProfiler就…
```R install.packages("gprofiler") library(gprofiler) ``` 然后,使用`gconvert`函数将gProfiler ID转换为基因名称: ```R # 创建一个包含gProfiler ID的向量 gprofiler_ids <- c("ENSG00000136997", "ENSG00000157764", "ENSG00000228253") # 将gProfiler ID转换为基因名称 gene_names <- gconvert(gpr...
How to cite:Kolberg L, Raudvere U, Kuzmin Iet al.gprofiler2 -- an R package for gene list functional enrichment analysis and namespace conversion toolset g:Profiler [version 2; peer review: 2 approved].F1000Research2020,9(ELIXIR):709 (https://doi.org/10.12688/f1000research.24956.2)First ...
g:Profiler ( https://biit.cs.ut.ee/gprofiler ) is a widely used gene list functional profiling and namespace conversion toolset that has been contributing to reproducible biological data analysis already since 2007. Here we introduce the accompanying R package, gprofiler2 , developed to facilita...
但是网页工具我用起来毕竟还是有些丢脸,所以安排学徒比较了一下常用的3大在线分析工具:Enrichr、WebGestalt、gprofiler与R包clusterprofiler,有了这个笔记分享给大家。 PART 01 Enrichr 网页版 enrichr由Ma'ayan Lab由2013年开发并维护,现引用量突破2500,而且很多都是CNS文章引用。现有来自164个库的332911个terms包括常规...
Visualization and differential analysis of protein expression data using R. Methods Mol. Biol. 1362, 105–118 (2016). CAS PubMed Google Scholar Schubert, O. T., Rost, H. L., Collins, B. C., Rosenberger, G. & Aebersold, R. Quantitative proteomics: challenges and opportunities in basic...
pip3 install -r requirements leads to: ERROR: Cannot install -r requirements.txt (line 14), -r requirements.txt (line 9) and requests==2.31.0 because these package versions have conflicting dependencies. The conflict is caused by: The user requested requests==2.31.0 curlify 2.2.1 depends ...
Molecular Signatures Database(MSigDB): GSEA工作组维护的基因集数据库,人类用的比较多,尤其是hallmakr基因集。 生化通路数据库 Reactome Panther NetPath HumanCyc National Cancer Institute Pathway Interaction Database KEGG 通路元数据库 Pathway Common