data-raw/get_data.R

In fungenomics/cytobox: A toolbox for analyzing single cell RNA-seq data

# Selin Jessa

# We repurpose data provided in the Seurat R package to provide a small dataset
# for testing and examples

pbmc <- Seurat::pbmc_small
markers_pbmc <- Seurat::FindAllMarkers(pbmc)
pbmc@project.name <- "pbmc"

usethis::use_data(pbmc)
usethis::use_data(markers_pbmc)

# Annotations
hg.genes <- fread("~/scratch/cortex/annotations/hg_gene_annotation.txt", data.table = FALSE)
mm.genes <- fread("~/scratch/cortex/annotations/mm_gene_annotation.txt", data.table = FALSE)
mm2hg.genes <- fread("~/scratch/cortex/annotations/mm_gene_annotation_hg_homol.txt", data.table = FALSE)
hg2mm.genes <- fread("~/scratch/cortex/annotations/hg_gene_annotation_mm_homol.txt", data.table = FALSE)

usethis::use_data(hg.genes)
usethis::use_data(mm.genes)
usethis::use_data(mm2hg.genes)
usethis::use_data(hg2mm.genes)