Computational Biology Laboratory, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark.
This GitHub repository was created for the The CAncer bioMarker Prediction Pipeline (CAMPP). A collection of R scripts made for computational prediction of serum cancer biomarkers.
The publication associated to CAMPP and to be cited in case of its usage is currently on biorxiv as a pre-print:
CAncer bioMarker Prediction Pipeline (CAMPP) - A standardised and user-friendly framework for the analysis of quantitative biological data. biorxiv, doi: https://doi.org/10.1101/608422
Thilde Terkelsen, Anders Krogh and Elena Papaleo
corresponding author: email@example.com
The pipeline consists of three R scrips which are currently run from the linux command-line using flags. The scrips are named:
CAMPPInstall.R CAMPPFunctions.R CAMPP.R
The CAMPPInstall.R script is run the first time the pipeline is used to ensure that all needed R-packages are installed.
The CAMPPFunctions.R script contains custum functions used for analysis and is sourced within the CAMPP.R. The CAMPPFunctions.R script should be located in the folder from which the pipeline is run.
The CAMPP.R script acts as the actual pipeline and is run with flags from the linux command-line. The flag -h is implemented for user help.
Data example used in the CAMPPManual.pdf is located at https://github.com/ELELAB/N-glycan-TIF with the original publication, in the folder https://github.com/ELELAB/N-glycan-TIF/tree/master/Data/DataExamples.