README.md

In regeneron-mpds/ICON: What the Package Does (One Line, Title Case)

ICON

ICON is an R package for identifing reliable TCR-pMHC interactions from multi-omics multiplexed multimer binding single cell sequencing data (Zhang et al. 2021).

Install and load ICON package:

devtools::install_github('regeneron-mpds/ICON') # R version >= 3.6.1
library('ICON')

Steps to run ICON:

Download the Demo Data in this repo for an example run.

Step 1: filter out low-quality cells based on scRNA data

rna.raw <- readRDS("path_to_demo_data/rna_raw.rds") # input single cell RNA-seq data
adt.raw <- readRDS("path_to_demo_data/adt_raw.rds") # input single cell dextramer data
pQC.data <- QC(rna.raw)
good.cells <- selectGoodCells(pQC.data, adt.raw)
test.data <- good.cells[15:58,] # extract test dextramer data
nc.data <- good.cells[59:64,] # extract negative control dextramer data

Step 2: select T cells with paired alpha and beta chains

tcr.all <- readRDS("path_to_demo_data/filtered_tcr_annotation.rds")
tcr.pair <- pair_TCR(tcr.all)

Step 3: identify pMHC binding T cells

bg <- estBgNoise(test.data, nc.data) # inspect background noise to choose cutoff
binders <- Identify_binders(test.data, tcr.pair, out_dir = path_to_output_files)

License

License can be found in the file LICENSE.

regeneron-mpds/ICON documentation built on Jan. 27, 2021, 8:02 p.m.