prepiscak/them6_gsea

# Them6 GSEA analysis

THEM6 GSEA analysis

About

Gene Set Enrichment Analysis (GSEA) and visualization for THEM6 project.

Blomme, A. et al. EMBO molecular medicine, 14(3), e14764. THEM6-mediated reprogramming of lipid metabolism supports treatment resistance in prostate cancer

Content

Main files:

• them6_gsea.Rmd - R notebook with R code used for the analysis.
• dockRstudio_v4.0.3_run.sh - bash script to start docker Rstudio server.
• them6_gsea_renv.lock - renv lock file with R packages specifications.
• generate_them6_report.sh - bash script to generate R notebook report; it requires that Rstudio server is running (dockRstudio_v4.0.3_run.sh) and new_port used is the same in both files.

Main folders:

• datasets - contains input RNA-seq results datasets.
• scripts - contains helper functions.
• results_dir - contains results from the analysis.

Usage

Clone the project repository

git clone https://github.com/prepiscak/them6_gsea.git

The them6_gsea folder contains all the code needed to reproduce the analysis. R dependencies can be managed either using the them6 docker image (preferred; see Requirements) or renv lock file (them6_gsea_renv.lock).

Preferred - interactive

Start Rstudio server and generate the analysis report manually.

1. Start Rstudio server

# new_port=7667
# username: rstudio
# password: them6
bash dockRstudio_v4.0.3_run.sh 

2. Go to localhost:7666 in your browser (Chrome, Firefox). This will open Rstudio server login page where default Username: rstudio and Password: them6
3. Open project file workspace.Rproj and once loaded open them6_gsea.Rmd file.
4. Run the analysis_parameters chunk to restore the R dependencies.
5. Use the "Knit" button to generate results and render the report and/or explore/run individual code chunks.

⚠️ analysis_parameters chunk (see point 4. above) needs to be run first otherwise you will get:

"Packages...not installed" 
or when using "Knit" button:
"Rendering R Markdown...requires...the following packages:..."

Preferred - automatic

Generate results and render report using generate_them6_report.sh script.

1. start Rstudio server

# new_port=7667
# username: rstudio
# password: them6
bash dockRstudio_v4.0.3_run.sh 

2. While the Rstudio server is running execute (in a separate terminal) generate_them6_report.sh - this will generate the results, them6_gsea.html and log file (generate_them6_report.log).

# new_port=7667 needs to be the same in:
#   dockRstudio_v4.0.3_run.sh and generate_them6_report.sh
bash generate_them6_report.sh

Local Rstudio + renv

1. Start local version of Rstudio
2. Open them6_gsea.Rmd
3. Use the "Knit" button to generate results and render the report and/or explore/run individual code chunks. R dependencies should be automatically restored from them6_gsea_renv.lock file.

Requirements

• Docker
• docker image for THEM6 project