GDSCtools

Dartmouth Genomic Data Science Core: General Utilities

Warning

🚧 In development:
This package currently supports basic single-cell quality control, differential expression analysis, ORA analysis, and pathway network analysis. More functionalities and utilities will be added, stay tuned!

Installation

# Install from github
devtools::install_github("https://github.com/Dartmouth-Data-Analytics-Core/GDSCtools")

Dependencies

CRAN: igraph, dplyr, ggplot2, ggwordcloud, patchwork, scales, stringr, purrr, ggExtra

Bioconductor: Seurat, clusterProfiler, org.Mm.eg.db (or org.Hs.eg.db)

Install Bioconductor dependencies first if needed:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(c("clusterProfiler", "org.Mm.eg.db"))

Vignettes

• Loading CellRanger outputs as Seurat Objects
• Basic Single Cell GEX Quality Control
• Pathway Network Analysis

License

MIT