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.
Credit
- Pathway enrichment in marker gene lists (
getEnrichedPathways()) is done through the enrichR API (https://github.com/wjawaid/enrichR). I took theenrichrfunction 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
