README.md

In Spaniel: Spatial Transcriptomics Analysis

Spaniel Spatial Transcriptomics Analysis

Spaniel is an R package for analysing Spatial Transcriptomics data.

Install dependencies:

Mac Only

xcode-select --install

All operating systems

DevTools

install.packages('devtools')

Seurat

Spaniel requires Seurat v3.0. This can be installed:

install.packages('Seurat')

SingleCellExperiment

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("SingleCellExperiment", version = "3.8")

Scater

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("scater", version = "3.8")

Install Spaniel:

install_github(repo = "RachelQueen1/Spaniel", 
                             build_opts = c("--no-resave-data", "--no-manual"), 
                             build_vignettes = TRUE)

View Vignette:

https://rachelqueen1.github.io/Spaniel_Documentation/

Spaniel documentation built on Nov. 8, 2020, 5:54 p.m.