Add module for BioQC
grst opened this issue · comments
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:
- heatmap
- table
Note: if another species than human is used, the gene symbols need to be mapped to human orthologs.
The method has been tested using this approach on rat and mouse, other mammalian species can be expected, to work, too.