In umccr/gpgr: Genomics Platform Group Reporting

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📚 gpgr - Genomics Platform Group Reporting

Contains reports and functions used in the Genomics Platform Group at the University of Melbourne Centre for Cancer Research.

• Docs: https://umccr.github.io/gpgr/

Installation

remotes::install_github("umccr/gpgr")

• Or if used inside a conda environment:

conda install r-gpgr -c umccr -c conda-forge -c bioconda

Main modules

🔮 PURPLE {#id_-purple}

• Read and process output files from the PURPLE purity/copy number estimator tool from the Hartwig Medical Foundation (https://github.com/hartwigmedical/hmftools/tree/master/purple). See vignette at https://umccr.github.io/gpgr/articles/purple.html.

sash {#id_-sash}

• Generate a HTML report with results from the sash WGS post-processing workflow
• https://github.com/scwatts/sash. See the CLI section below for options.

🥳 Developers {#id_-developers}

See https://umccr.github.io/gpgr/articles/devnotes.html for developer notes.

💻 CLI {#id_-cli}

A gpgr command line interface is available for convenience.

• If you're using the conda package, the gpgr.R command will already be set up inside an activated conda environment.
• If you're not using the conda package, you need to export the gpgr/inst/cli/ directory to your PATH in order to use gpgr.R.

```{bash eval=FALSE} gpgr_cli=$(Rscript -e 'x = system.file("cli", package = "gpgr"); cat(x, "\n")' | xargs) export PATH="${gpgr_cli}:${PATH}"

```{bash prompt=TRUE, echo=FALSE}
gpgr_cli=$(Rscript -e 'x = system.file("cli", package = "gpgr"); cat(x, "\n")' | xargs)
export PATH="${gpgr_cli}:${PATH}"
echo "gpgr.R --version" & gpgr.R --version
echo ""
echo "#-----------------------------------#"
echo "gpgr.R --help" & gpgr.R --help
echo ""
echo "#-----------------------------------#"
echo "#------- Cancer Report -------#"
echo "gpgr.R canrep --help" & gpgr.R canrep --help
echo ""
echo "#-----------------------------------#"

umccr/gpgr documentation built on Aug. 22, 2024, 9:51 p.m.