Bioconductor Code: BulkSignalR (original) (raw)

# 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 LR*db* database, which was previously included in our other package **SingleCellSignalR**, available from Bioconductor [here](https://www.bioconductor.org/packages/release/bioc/html/SingleCellSignalR.html). 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 ``` R # 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](https://github.com/ZheFrench/BulksignalR/blob/master/NEWS). **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](https://github.com/ZheFrench/BulksignalR/blob/master/LICENSE.md) License. [\](https://shields.io/)