In unistbig/CellEnrich: Pathway Enrichment Analysis, Visualize for Single Cell Data

knitr::opts_chunk$set(
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Introduction

• Testing Environment

• Windows 10

• R version 4.0
• Rstudio 1.2.5042

• Rtools 40

• This installation guide is written in latest version of R (4.0).

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 package first, to install following packages in Github / Bioconductor (not in CRAN).

library(devtools)
library(BiocManager)

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As noted in README

CellEnrich needs some packages to be installed before use it.

Bioconductor Packages

1. SingleCellExperiment
2. scran

BiocManager::install('SingleCellExperiment')
BiocManager::install('scran')

Other Packages

1. waiter
2. ggbiplot

devtools::install_github('JohnCoene/waiter')
devtools::install_github('vqv/ggbiplot')

After install these 3 packages,

Install CellEnrich

running this Script will install most of dependent packages.

install_github('unistbig/CellEnrich')
library(CellEnrich)

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Download Example Data

CellEnrich provides example dataset and gene-sets.

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

CellEnrich::DownloadData()

Here are list of data.

• Human Gene-sets

• "c2v7.RData" ( Curated )

• "humanGO.RData"
• "humanGOBP.RData"
• "humanGOCC.RData"
• "humanGOMF.RData"

• "keggv7.RData" ( KEGG )

• Mouse Gene-sets

• "mouseGO.RData"

• "mouseGOBP.RData"
• "mouseGOCC.RData"
• "mouseGOMF.RData"

• "mouseKEGG.RData"

• Human Data

• Seurat PBMC Guide

• "pbmcClustInfo.RData"

• "pbmcData.RData"

• DuoClustering

• paper

• "koh.RData"

• "kohInfo.RData"

• Mouse Data

• Seurat Mouse Guide

unistbig/CellEnrich documentation built on July 27, 2020, 12:52 p.m.