Oncology BIomaRker Discovery (OncoBird)

Prerequisites

The OncoBird shiny application runs in a local virtual docker environment. A Bioconductor package is currently in progress, but is already publicly available, for instructions regarding its installation see code/OncoBird/.

Running the OncoBird shiny application with docker

After starting docker, you can pull the docker image for OncoBird by typing:

docker pull aljoshoh/oncobird_shiny

Finally, run the image by:

docker run --rm -p 3838:3838 aljoshoh/oncobird_shiny

Now you can navigate to 127.0.0.1:3838 in a browser for executing OncoBird. If you want to build your own container, run ./environment/make_docker.sh

Data input format

The molecular and the clinical data for running OncoBird can be jointly in one data frame, or supplied as clinical data and mutational data separately. Thereby, the following format is expected.

data/data_mutations.csv

sample	<MUT1>_AMP	<MUT2>_SV	<MUT3>_DEL
<X1>	1	1	1
<X2>	1	0	0
<X3>	0	1	0
<X4>	0	0	0
...	...	...	...

data/data_clinical.csv

sample	treatment	<subtype1>	<subtype2>	<OS/PFS>.event	<OS/PFS>.months	ORR
<X1>	t1	C1	left	0	11	0
<X2>	t1	C2	right	0	22	1
<X3>	t2	C2	left	0	33	1
<X4>	t2	C2	left	1	44	1
...		...	...	...	...	...

Reference

For citing OncoBird, please refer to the original manuscript https://doi.org/10.1038/s41467-023-41011-4:

Ohnmacht A.J. et al. The Oncology Biomarker Discovery framework reveals cetuximab and bevacizumab response patterns in metastatic colorectal cancer. Nat. Commun., 14(1) 2023