CellEnrich

Pathway enrichment analysis / visualize for Single Cell Data

Online manual is available in here

🔧 Install

if(!require(remotes)){
  install.packages('remotes') # install devtools if not installed.
}
remotes::install_github('vqv/ggbiplot')
remotes::install_github('unistbig/cellenrich')
library(CellEnrich)

🚢 Example run with PBMC data

# download minimal data to working directory

download.file('https://github.com/jhk0530/CellEnrich/blob/master/pbmcData.RData?raw=true','pbmcData.RData', mode = 'wb')
download.file('https://github.com/jhk0530/CellEnrich/blob/master/pbmcClustinfo.RData?raw=true','pbmcClustinfo.RData', mode = 'wb')
download.file('https://github.com/jhk0530/CellEnrich/blob/master/humanKEGG.RData?raw=true', 'humanKEGG.RData', mode = 'wb')

# load library and data

library(CellEnrich)
load("pbmcClustInfo.RData")
load("pbmcData.RData")


CountData <- pbmcData
GroupInfo <- pbmcClustInfo
rm(pbmcData, pbmcClustInfo) # remove .

# Run cellenrich
CellEnrich(CountData, GroupInfo)

📎 Dependency

• dplyr - 0.8.5
• DT - 0.13
• ggplot2 - 3.3.0
• ggrepel - 0.8.2
• highcharter - 0.7.0.9001
• htmltools - 0.4.0
• magrittr - 1.5
• Rtsne - 0.15
• scales - 1.1.0
• scran - 1.14.6
• Seurat - 3.2.0
• shiny - 1.4.0.2
• shinyFeedback - 0.2.0
• shinyjs - 1.1
• shinymaterial - 1.0.1
• SingleCellExperiment - 1.8.0
• sortable - 0.4.2
• uwot - 0.1.8
• waiter - 0.1.1.9000

😊 Authors

• Jinhwan Kim @jhk0530
• prof. Dougu Nam dougnam@unist.ac.kr

📝 License

This project is MIT licensed