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BioQC is a method to detect tissue heterogeneity in gene expression data (Zhang et al., BMC Genomics, 2017). Enrichment for unexpected tissues can be a consequence of mislabeled samples, technical reasons (e.g. imperfect dissection) or biological reasons (e.g. immune infiltration).
In biokitr:
- 378 tissue-specific gene signatures derived from public and in-house data are considered
- Signatures are tested for enrichment in highly expressed genes for each sample using the Wilcoxon-Mann-Whitney test
- Enrichment scores Q are defined based on the -log10(p-value)
- Signatures with Q > 2 in at least one sample are shown in the heatmap (the top 40 if there are more)
Internal information:
See https://drive.google.com/file/d/18U_ShdB0ATSWSwdXohUvlA3aC4ZnRmWE/view minute 17
BEDA/biokitr/blob/ab4c130410539f51fbfe680b7e5bc93f5a5163e7/R/gse_bioqc.R#L24
BEDA/biokitr/blob/ab4c130410539f51fbfe680b7e5bc93f5a5163e7/R/gse_bioqc.R#L67
To do: just design.
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