Gene Set Enrichment Analysis (GSEA) and visualization for THEM6 project.
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
) andnew_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.
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
).
Start Rstudio server and generate the analysis report manually.
- Start Rstudio server
# new_port=7667
# username: rstudio
# password: them6
bash dockRstudio_v4.0.3_run.sh
- Go to
localhost:7666
in your browser (Chrome, Firefox). This will open Rstudio server login page where defaultUsername: rstudio
andPassword: them6
- Open project file
workspace.Rproj
and once loaded openthem6_gsea.Rmd
file. - Run the
analysis_parameters
chunk to restore the R dependencies. - 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:..."
Generate results and render report using generate_them6_report.sh
script.
- start Rstudio server
# new_port=7667
# username: rstudio
# password: them6
bash dockRstudio_v4.0.3_run.sh
- 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
- Start local version of Rstudio
- Open
them6_gsea.Rmd
- Use the
"Knit"
button to generate results and render the report and/or explore/run individual code chunks. R dependencies should be automatically restored fromthem6_gsea_renv.lock
file.