README.md

SIFT-seq data for patient 0606T1

R data package related to

Chandran et al. Immunogenicity and therapeutic targeting of a public neoantigen derived from mutated PIK3CA Nat Medicine (2022).

This package contains access to the processed TCR-seq and scRNA-seq data of T cells obtained from patient 0606T1.

How to use it

## install
devtools::install_github("abcwcm/Klebanoff0606T1")

Upon installation, the processed data, e.g. in the form of SingleCellExperiment objects, can be loaded thus:

## load SingleCellExperiment objects
sce.0606 <- Klebanoff0606T1::load_0606T1shared()

## load results of differential gene expression comparisons
## see 
Klebanoff0606T1::load_DE_results() # loads an object named `delist.both`
de.0606 <- delist.both; rm(delist.both)

For more details, see the code repository and the Rmd files detailing how the data underlying the figures were obtained.