BRETIGEA - Brain Cell Type Specific Gene Expression Analysis
Analysis of relative cell type proportions in bulk gene
expression data. Provides a well-validated set of brain cell
type-specific marker genes derived from multiple types of
experiments, as described in McKenzie (2018)
<doi:10.1038/s41598-018-27293-5>. For brain tissue data sets,
there are marker genes available for astrocytes, endothelial
cells, microglia, neurons, oligodendrocytes, and
oligodendrocyte precursor cells, derived from each of human,
mice, and combination human/mouse data sets. However, if you
have access to your own marker genes, the functions can be
applied to bulk gene expression data from any tissue. Also
implements multiple options for relative cell type proportion
estimation using these marker genes, adapting and expanding on
approaches from the 'CellCODE' R package described in Chikina
(2015) <doi:10.1093/bioinformatics/btv015>. The number of cell
type marker genes used in a given analysis can be increased or
decreased based on your preferences and the data set. Finally,
provides functions to use the estimates to adjust for
variability in the relative proportion of cell types across
samples prior to downstream analyses.
