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https://github.com/jcolinge/BulkSignalR

BulkSignalR
https://github.com/jcolinge/BulkSignalR

Last synced: 4 months ago
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BulkSignalR

Host: GitHub
URL: https://github.com/jcolinge/BulkSignalR
Owner: jcolinge
License: other
Created: 2020-05-25T13:15:48.000Z (about 4 years ago)
Default Branch: master
Last Pushed: 2023-12-30T12:26:00.000Z (6 months ago)
Last Synced: 2024-02-27T11:19:08.860Z (4 months ago)
Language: R
Size: 39.5 MB
Stars: 8
Watchers: 2
Forks: 3
Open Issues: 6
Metadata Files:
- Readme: README.md
- License: LICENSE

Lists

awesome-cell-cell-communication - BulkSignalR - [R]- BulkSignalR is a R package to infer ligand-receptor networks with downstream pathways from bulk data or spatial data (localized bulk data). (Uncategorized / Uncategorized)

README

        
# BulkSignalR 

[![CRAN Version](https://www.r-pkg.org/badges/version/BulkSignalR)](https://cran.r-project.org/package=BulkSignalR)

[![CRAN Downloads](https://cranlogs.r-pkg.org/badges/BulkSignalR)](https://cran.r-project.org/package=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 is  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 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")

```

## Notes

For a version history/change logs, see the [NEWS file](https://github.com/jcolinge/BulksignalR/blob/master/NEWS.md).

**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](https://github.com/jcolinge/BulksignalR/blob/master/LICENSE.md) License.

[![Generic badge](https://img.shields.io/badge/License-CeCILL-green.svg)](https://shields.io/)