PDO_BME_EKGel

Introduction

This is a project to regenerate the RNAseq compariosn between PDOs clutured in two mediums in this paper: "Biomimetic hydrogel supports initiation and growth of patient-derived breast tumor organoids" citation's info to be added

The script for the analysis is written in R.

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Dependencies:

These R packages need to be installed in order to run the analysis script:

• Biobase
• ggrepel
• ggplot2
• ComplexHeatmap
• circlize
• DESeq2
• snowfall
• GSA
• piano

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Reproducibility of the Analysis:

• Once the project is downloaded to the user computer, the user needs to navigate to the main directory of the project "PDO_BME_EKGel-master".
• Inside the main directory, there is an R script file named "analysis.R". Running this script will regenerate the RNAseq compariosn between PDOs clutured in two mediums in this paper.

Important Note: the user needs to set the working directory inside the script file before running it, i.e. change the following code inside the script:

setwd("PDO_BME_EKGel") # set to path of cloned project in your machine

• Included in the project are:

  1- RNAseq processed data for all PDOs clutured in different mediums, Data/UHN_BR_PDOs_hg38_kallisto_mixed.rda.

  2- REACTOME genesets used for the pathway analysis, Data/c2.cp.reactome.v7.4.symbols.gmt.