How to install CellEnrich

Hai Nguyen

2024.06.20

Introduction

  • Testing Environment
  1. Ubuntu 22.04.2 LTS
  2. R version 4.2.0
  3. RStudio 2023.03.0+386 “Cherry Blossom”
  4. Rtools 40
  • This installation guide is written in R version 4.2.0

Install Dependent Packages

  • Also some package needs install from sources which needs compilation and it needs proper version of Rtools installed

  • It’s recommended to install devtools, BiocManager packages first, to install following packages in Github / Bioconductor (not in CRAN).

library(devtools)
library(BiocManager)

As noted in README

CellEnrich needs some packages to be installed before using it.

Bioconductor Packages

  1. SingleCellExperiment
  2. scran
BiocManager::install('SingleCellExperiment')
BiocManager::install('scran')

Other Packages

  1. waiter
  2. ggbiplot
  3. farver
devtools::install_github('JohnCoene/waiter')
devtools::install_github('vqv/ggbiplot')
install.packages('farver') # install 'farver' if not installed.

remotes::install_github('noobCoding/CellEnrich')

After installing these packages:

Install CellEnrich

Running this Script will install most of the dependent packages.

install_github('noobCoding/CellEnrich')

library(CellEnrich)

Download Data

CellEnrich provides example data and genesets.

using this function, users can download them in the current working directory.

CellEnrich::DownloadData(type='test') # for available human related data & genesets 

## Use type='all' for all available data

Here is a list of data.

  • Human Gene-sets

    • “Reactome_2022.RData”
    • “WikiPathways_2021_Human.RData”
    • “KEGG_2021_Human.RData”
    • “humanGO.RData”
    • “humanGOBP.RData”
    • “humanGOCC.RData”
    • “humanGOMF.RData”

  • Mouse Gene-sets

    • “WikiPathways_2019_Mouse.RData”
    • “KEGG_2021_Mouse.RData”
    • “mouseGO.RData”
    • “mouseGOBP.RData”
    • “mouseGOCC.RData”
    • “mouseGOMF.RData”

  • Human Data

  • Mouse Data

License

Developers

  • Hai Nguyen
    Author, maintainer