R package upon which the Cerebro is built.
Contains helper function that prepare single-cell RNA-seq data stored in a Seurat object for visualization in Cerebro.
Seurat v3 and SCE
/SingleCellExperiment
objects are supported.
Make sure to install the package using BiocManager::install()
because devtools::install_github()
will otherwise pull old versions of dependencies that can result in errors.
BiocManager::install('romanhaa/cerebroApp')
For further details, please refer to the official cerebroApp website.
- Pathway enrichment in marker gene lists (
getEnrichedPathways()
) is done through the enrichR API (https://github.com/wjawaid/enrichR). I took theenrichr
function and modified it to run in parallel (future_lapply
) and not print status messages. - Gene set enrichment analysis (
performGeneSetEnrichmentAnalysis()
) is performed using the GSVA R package. p- and q-value statistics are calculated through the same method as used by "Evaluation of methods to assign cell type labels to cell clusters from single-cell RNA-sequencing data", Diaz-Mejia et al., F1000Research (2019). Link to publication