This repository contains the PIC-seq all the needed code and metadata files to analyze and generate figures for Cohen M. & Giladi A. et al. Nature Cancer 2022

In order to run the scripts, download processed data from GSE160903 to the folder output/umi.tab

Unzip and change file names by running these shell commands (in output/umi.tab): gzip -d * ls -1 | awk -F'_' '{print $0,$2}' | xargs -n 2 mv

Download published data into their respective folders: GSE123139 output/published_data/melanoma/ EGAD00001006608 output/published_data/breast/ GSE135382 output/published_data/pic-seq/

To start analysis, run from the root directory: Rscript scripts/run.r

Please send questions to Amir Giladi: aygoldberg@gmail.com

Required R packages:

Package version glmnet 2.0-16 foreach 1.4.4 Matrix 1.2-18 compositions 1.40-2 bayesm 3.1-0.1 energy 1.7-5 robustbase 0.93-3 tensorA 0.36.1 gplots 3.0.1.1 plotrix 3.7-4 plyr 1.8.4 RANN 2.6.1 reshape2 1.4.3 KernSmooth 2.23-15 dendextend 1.9.0 Hmisc 4.2-0 Formula 1.2-3 survival 3.2-3 lattice 0.20-38 tglkmeans 0.2.0 ggrepel 0.8.1 ggplot2 3.3.2.9000 ape 5.2 scales 1.0.0 metacell 0.3.41 tgstat 2.3.5 misha 4.0.10