README.md

In ncborcherding/scone: Single-Cell Operation for Neat Enrichment

scone

Single-cell Operation for Neat Enrichment

scone has been replaced by escape R package, available on github and bioconductor.

Introduction

Single-cell sequencing (SCS) is an emerging technology in the across the diverse array of biological fields. Part of the struggle with the high-resolution approach of SCS, is distilling the data down to meaningful scientific hypotheses. scone was created to bridge SCS results, either from raw counts or from the popular Seurat R package, with gene set enrichment analyses (GSEA), allowing users to simply and easily graph outputs. The package contains the whole Molecular Signature Database v7.0 and enables users to select single gene sets, multiple gene sets, and even libraries to perform enrichment analysis on.

R Packages Required

• dplyr
• facoextra devtools::install_github("kassambara/factoextra")
• ggplots2
• ggrepel
• ggridges
• grDevices
• GSEABase
• GSVA
• pheatmap
• rlang
• Seurat

Installation

devtools::install_github("ncborcherding/scone")

Learning To Use scone:

Vignette available here, includes almost 2,000 T cells across from a previous cutaneous T cell lymphoma paper.

Contact

Questions, comments, suggestions, please feel free to contact Nick Borcherding via this repository, email, or using twitter.

ncborcherding/scone documentation built on Sept. 5, 2020, 1:11 a.m.