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Add module for BioQC #15

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grst opened this issue Nov 17, 2021 · 1 comment
Open

Add module for BioQC #15

grst opened this issue Nov 17, 2021 · 1 comment

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@grst
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grst commented Nov 17, 2021

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
@grst
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grst commented Nov 17, 2021

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.

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