BioQC performs signature enrichment for tissue signatures. This allows to check if e.g. samples have been swapped, or contaminations happend during sample handling.
Repo:
https://github.com/Accio/BioQC
Example code, you can use something similar in the pipeline (currently in private gitlab):
https://gitlab.i-med.ac.at/icbi-lab/ibdome/ibdome-projects/-/blob/2b1e4b4499d731293feebc8266510004b5f423a4/subprojects/data-overview-for-grant-application/13_plots_for_zlatko.Rmd#L70-120
Input:
- gene expression matrix
- sample sheet
Output:
BioQC performs signature enrichment for tissue signatures. This allows to check if e.g. samples have been swapped, or contaminations happend during sample handling.
Repo:
https://github.com/Accio/BioQC
Example code, you can use something similar in the pipeline (currently in private gitlab):
https://gitlab.i-med.ac.at/icbi-lab/ibdome/ibdome-projects/-/blob/2b1e4b4499d731293feebc8266510004b5f423a4/subprojects/data-overview-for-grant-application/13_plots_for_zlatko.Rmd#L70-120
Input:
Output: