aba_marker_expression

<p>Filtered data set to only contain brain marker genes as well as ~100 other genes. The total data set can be downloaded by following the links in the original paper.</p>

datasets

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.

Andrew McKenzie

BRETIGEA

Brain Cell Type Specific Gene Expression Analysis

aba_marker_expression function

<p>An object of class <code>data.frame</code> with 395 rows and 377 columns.</p>

aba_marker_expression: Normalized FPKM expression data from a subset of the Allen Brain Atlas Aging, Dementia, and TBI study.

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