Last updated: 2023-02-17

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Knit directory: TranscriptDE-wf/analysis/

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File Version Author Date Message
html b8e3979 Pedro Baldoni 2023-02-17 Build site.
Rmd 9b96d31 Pedro Baldoni 2023-02-17 Cleanup main page
Rmd 89baa56 Pedro Baldoni 2023-02-17 Adding simulation how-to
html 89baa56 Pedro Baldoni 2023-02-17 Adding simulation how-to

The R code used in our simulation study to generate the simulated data, quantify the FASTQ files, run DTE methods, and summarize the results was organized as an R package and it is located in the GitHub repository of this page in the directory ./code/pkg.

To run our simulations, users should refer to the files stored in the directory ./code/simulation. The text file ./code/simulation/readme.txt presents the necessary steps to run the simulations and summarize the results, which can be briefly summarized as:

  1. Run the file parameters.R with, for example, the command Rscript parameters.R.

  2. Run the SLURM script run.sh with, for example, sbatch run.sh on your HPC running the SLURM workload manager. If your HPC uses a different workload manager, please change run.sh accordingly.

  3. Once all simulations have been completed, run the script summarize.R with, for example, the command Rscript summarize.R to summarize all the results.

Once steps 1-3 above have been completed, the Rmarkdown simulation-*.Rmd files under ./analysis can be run.