A function that assists with integration of bulk DE results tables with pre-processed scRNA-seq datasets available on Bioconductor, for downstream visualization tasks. The user is prompted to pick a scRNA-seq dataset from a menu. The output of the function is a list with the original results table, bulk gene counts, and the SingleCellExperiment object selected by the user.
a results table, as produced via
a DESeqDataSet with the bulk gene expression data (should contain gene-level counts)
This function assists the user in choosing a datset from a menu of options
that are selected based on the organism of the current dataset.
Currently only human and mouse bulk and single-cell RNA-seq datasets
are supported, and it is assumed that the bulk DE dataset has GENCODE
or Ensembl gene identifiers. Following the selection of the scRNA-seq
dataset, visualization can be performed with a package
which can be installed with
list containing: res, dds, and a SingleCellExperiment as selected by the user
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