Installation Instructions
Essentials
- Install R, version 3.4 or greater
- (Optional) Highly recommend install RStudio
- Install LinQ-View from github
if (!require("devtools")) {install.packages("devtools")}
devtools::install_github("WilsonImmunologyLab/LinQView",dependencies = TRUE)
Potential installation issue with R 4.0
Because this package developed some C++ codes with Rcpp library, R 4.0 users may have installation issues with this package. The error message usually be:
fatal error: 'math.h' file not found
For Windows RStudio users, we suggest you switch back to R 3.6.
For Mac RStudio users, we highly recommand a tool RSwitch that allows you to keep multiple R version and switch among them.
Dependencies
Most of dependencies can be installed when install LinQ-View, some packages may need to be installed seprately. Users can copy the all-in-one command collections below:if(!require("Seurat")) install.packages("Seurat")
if(!require("dplyr")) install.packages("dplyr")
if(!require("ggplot2")) install.packages("ggplot2")
if(!require("cowplot")) install.packages("cowplot")
if(!require("FastKNN")) install.packages("FastKNN")
if(!require("reshape2")) install.packages("reshape2")
if(!require("umap")) install.packages("umap")
if(!require("igraph")) install.packages("igraph")
if(!require("emstreeR")) install.packages("emstreeR")
if(!require("scales")) install.packages("scales")
if(!require("Rtsne")) install.packages("Rtsne")
if(!require("Rcpp")) install.packages("Rcpp")
if(!require("tidyverse")) install.packages("tidyverse")
devtools::install_github("PaulingLiu/ROGUE")
Click to show a detailed list of all dependencies and installation tips.