BulkSignalR

Overview

BulkSignalR is used to infer ligand-receptor (L-R) interactions from bulk expression (transcriptomics/proteomics) data, or spatial transcriptomics.

Potential L-R interactions are taken from the LRdb database, which was previously included in our other package SingleCellSignalR, available from Bioconductor here.

Inferences rely on a statistical model linking potential L-R interactions with biological pathways from Reactome or biological processes from GO.

A number of visualization and data summary functions are proposed to help navigating the predicted interactions.

Installation

# 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("ZheFrench/BulkSignalR",build_vignettes = TRUE)

# To read the vignette
# browseVignettes("BulkSignalR")

Notes

For a version history/change logs, see the NEWS file.

BulkSignalR has been successfully installed on Mac OS X, Linux, and Windows using R version 4.4.

The code in this repository is published with the CeCILL License.