This repository contains our first version of the library as published in Nucleic Acids Research in 2023. Meanwhile, we added the library to Bioconductor, which required slight modifications to fulfill Bioconductor standards.
The current version of the library (the one in Bioconductor) can be found here. It is temporarily developed from another GitHub repository and it will ultimately be integrated back into this one. Until then, this very repository should be considered for the first version only.
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 is 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.
# BulkSignalR is not included in BioConductor yet.
# 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.
BulkSignalR has been successfully installed on Mac OS X, Linux, and Windows using R version 4.2.
The code in this repository is published with the CeCILL License.
