Companion repository to SingleCellSignalR (Version 2)
This companion repository to Version 2 of the Bioconductor
SingleCellSignalR
library, we illustrate its usage with more flexibility than in the vignette or
the on-line documentation. In particular, we provide a basic example that
illustrates how a single-cell data set can be analyzed, which may serve as
starting point to write your own code.
We also provide three additional example scripts addressing particular data types that are now amenable to SingleCellSignalR analysis:
- Single-cell proteomics data (scProt-MS);
- Bulk RNA-seq data obtained from FACS-separated cell populations;
- PDX bulk RNA-seq data that were aligned against both a human and a murine reference genome to separate cancer and stromal components.
These particular data types are discussed in our latest paper about
version 2 of SingleCellSignalR.
Note that Version 2 of SingleCellSignalR is a complete re-design,
which now relies on new S4 classes and on our other library
BulkSignalR
that is used as foundation layer. Therefore, the usage of SingleCellSignalR
compared to the initial Version 1 has completely changed. Nonetheless,
the original scoring scheme LR-score is still available with the
new implementation.