title	author	date	package	abstract	output	bibliography	always_allow_html	vignette
Gene Set Enrichment Analysis	name affiliation email Wenching Calvin Chan, Ph.D. Center for Research Informatics, University of Chicago, Chicago, IL 60637 [email protected]	21 February, 2019	Gene Set Enrichment Analysis	- TBC	html_document theme highlight number_sections df_print toc toc_depth toc_float keep_md united tango true paged true 3 collapsed smooth_scroll true false true	GSEA.bib	true	%\VignetteIndexEntry{GSEA} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8}

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Enrichment Analysis

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• clusterProfiler: statistical analysis and visualization of functional profiles for genes and gene clusters

What is GeneRatio and BgRatio?

Figure 1: GeneRatio & BgRatio in clusterProfiler GeneRatio = $\frac{M}{N}$ & BgRatio = $\frac{k}{n}$

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Session information

## R version 3.5.1 (2018-07-02)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS  10.14.3
## 
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
## 
## attached base packages:
## [1] grid      stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
## [1] captioner_2.2.3.9000 dplyr_0.7.8          png_0.1-7           
## [4] kableExtra_1.0.1     knitr_1.21          
## 
## loaded via a namespace (and not attached):
##  [1] Rcpp_1.0.0         BiocManager_1.30.4 pillar_1.3.1      
##  [4] compiler_3.5.1     bindr_0.1.1        tools_3.5.1       
##  [7] digest_0.6.18      evaluate_0.12      tibble_2.0.1      
## [10] viridisLite_0.3.0  pkgconfig_2.0.2    rlang_0.3.1       
## [13] rstudioapi_0.9.0   yaml_2.2.0         xfun_0.4          
## [16] bindrcpp_0.2.2     httr_1.4.0         stringr_1.3.1.9000
## [19] xml2_1.2.0         hms_0.4.2          webshot_0.5.1     
## [22] tidyselect_0.2.5   glue_1.3.0         R6_2.3.0          
## [25] rmarkdown_1.11     readr_1.3.1        purrr_0.3.0       
## [28] magrittr_1.5       scales_1.0.0       htmltools_0.3.6   
## [31] assertthat_0.2.0   rvest_0.3.2        BiocStyle_2.10.0  
## [34] colorspace_1.4-0   stringi_1.2.4      munsell_0.5.0     
## [37] crayon_1.3.4

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Reference