BulkSignalR is used to infer ligand-receptor (L-R) interactions from bulk expression (transcriptomics/proteomics) data, or medium resolution spatial transcriptomics such as the 10x Genomics Visium platform. Particular types of bulk data are also supported such as purified cell populations transcriptomics and proteomics, or PDX mRNA-sequencing.
Known L-R interactions are taken from the LRdb database, which was previously included in our other package SingleCellSignalR, also available from Bioconductor here. Now, LRdb is distributed and updated separately.
Inferences rely on a statistical model linking potential L-R interactions with biological pathways downstream the receptor as defined in Reactome or GO Biological Processes.
A number of visualization and data summary functions are proposed to help navigating the predicted interactions.
Note that due to BulkSignalR introduction in Bioconductor, we modified certain class definitions and functions to adhere to Bioconductor standards. An overview of changes in BulkSignalR usage compared to early versions is provided in the companion project: BulkSignalR_companion.
# BulkSignalR directly from Bioconductor.
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("BulkSignalR")
# or Installation goes via GitHub:
# install.packages("devtools")
devtools::install_github("jcolinge/BulkSignalR",build_vignettes = TRUE)
# To read the vignette
# browseVignettes("BulkSignalR")
For a version history/change logs, see the NEWS file.
Previous versions of BulkSignalR (before introduction in Bioconductor) are availabe in the branch named before_BC at GitHub.com/jcolinge/BulkSignalR.
BulkSignalR has been successfully installed on Mac OS X, Linux, and Windows using R version 4.5.
The code in this repository is published with the CeCILL License.
