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.
These R packages need to be installed in order to run the analysis script:
- Biobase
- ggrepel
- ggplot2
- ComplexHeatmap
- circlize
- DESeq2
- snowfall
- GSA
- piano
- 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
.