BulkSignalR
This is the development version of BulkSignalR; for the stable release version, see BulkSignalR.
Infer Ligand-Receptor Interactions from bulk expression (transcriptomics/proteomics) data, or spatial transcriptomics
Bioconductor version: Development (3.22)
Inference of ligand-receptor (LR) interactions from bulk expression (transcriptomics/proteomics) data, or spatial transcriptomics. BulkSignalR bases its inferences on the LRdb database included in our other package, SingleCellSignalR available from Bioconductor. It relies on a statistical model that is specific to bulk data sets. Different visualization and data summary functions are proposed to help navigating prediction results.
Author: Jacques Colinge [aut]
, Jean-Philippe Villemin [cre]
Maintainer: Jean-Philippe Villemin <jpvillemin at gmail.com>
citation("BulkSignalR")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("BulkSignalR")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("BulkSignalR")| BulkSignalR-Configure | HTML | R Script |
| BulkSignalR-Differential | HTML | R Script |
| BulkSignalR-Main | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Network, NetworkInference, Proteomics, RNASeq, Software, Spatial, Transcriptomics |
| Version | 1.1.5 |
| In Bioconductor since | BioC 3.21 (R-4.5) (0.5 years) |
| License | CeCILL | file LICENSE |
| Depends | R (>= 4.5) |
| Imports | BiocFileCache, httr2, RCurl, cli, curl, rlang, jsonlite, matrixStats, methods, doParallel, glmnet, ggalluvial, ggplot2, gridExtra, grid, Rtsne, ggrepel, foreach, multtest, igraph, orthogene, stabledist, circlize (>= 0.4.14), ComplexHeatmap(>= 2.0.0), stats, scales, RANN, SpatialExperiment, SummarizedExperiment, tools |
| System Requirements | |
| URL | https://github.com/ZheFrench/BulkSignalR |
| Bug Reports | https://github.com/ZheFrench/BulkSignalR/issues |
See More
| Suggests | knitr, markdown, rmarkdown, STexampleData, testthat (>= 3.0.0), codetools, Matrix, lattice, cluster, survival, MASS, nlme |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | SingleCellSignalR |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | BulkSignalR_1.1.5.tar.gz |
| Windows Binary (x86_64) | BulkSignalR_1.1.4.zip |
| macOS Binary (x86_64) | BulkSignalR_1.1.5.tgz |
| macOS Binary (arm64) | BulkSignalR_1.1.5.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/BulkSignalR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/BulkSignalR |
| Bioc Package Browser | https://code.bioconductor.org/browse/BulkSignalR/ |
| Package Short Url | https://bioconductor.org/packages/BulkSignalR/ |
| Package Downloads Report | Download Stats |