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License: MIT Lifecycle: retired Twitter

⚠️ Discontinuation notice: Sadly, Cerebro and cerebroApp are no longer in active development. See here for more info.

cerebroApp

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 the enrichr 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