Package: BRETIGEA 1.0.4

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.

Authors:Andrew McKenzie [aut, cre], Minghui Wang [aut], Bin Zhang [aut]

BRETIGEA_1.0.4.tar.gz
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BRETIGEA.pdf |BRETIGEA.html
BRETIGEA/json (API)

# Install 'BRETIGEA' in R:
install.packages('BRETIGEA', repos = c('https://andymckenzie.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/andymckenzie/bretigea/issues

Datasets:
  • aba_marker_expression - Normalized FPKM expression data from a subset of the Allen Brain Atlas Aging, Dementia, and TBI study.
  • aba_pheno_data - Phenotype data from brain samples in the Allen Brain Atlas Aging, Dementia, and TBI study.
  • kelley_df_brain - Marker genes estimated from
  • markers_df_brain - Marker genes estimated from a meta-analysis of brain cell gene expression data from both humans and mice.
  • markers_df_human_brain - Marker genes estimated from a meta-analysis of brain cell gene expression data from humans only.
  • markers_df_mouse_brain - Marker genes estimated from a meta-analysis of brain cell gene expression data from mice only.

On CRAN:

cell-typegene-expressiongene-expression-signatures

6.17 score 14 stars 30 scripts 174 downloads 7 mentions 4 exports 0 dependencies

Last updated 11 months agofrom:b93da3fd0e. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 01 2024
R-4.5-winOKNov 01 2024
R-4.5-linuxOKNov 01 2024
R-4.4-winOKNov 01 2024
R-4.4-macOKNov 01 2024
R-4.3-winOKNov 01 2024
R-4.3-macOKNov 01 2024

Exports:adjustBrainCellsadjustCellsbrainCellsfindCells

Dependencies:

Brain cell type proportion analysis using BRETIGEA

Rendered fromBRETIGEA_basic.Rmdusingknitr::rmarkdownon Nov 01 2024.

Last update: 2023-12-27
Started: 2018-09-10