BulkSignalR
This is the released version of BulkSignalR; for the devel version, see BulkSignalR.
Infer Ligand-Receptor Interactions from bulk expression (transcriptomics/proteomics) data, or spatial transcriptomics
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | 1.4.0 |
| In Bioconductor since | BioC 3.21 (R-4.5) (1.5 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/jcolinge/BulkSignalR |
| Bug Reports | https://github.com/jcolinge/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_1.4.0.tar.gz |
| Windows Binary (x86_64) | BulkSignalR_1.4.0.zip |
| macOS Binary (big-sur-x86_64) | BulkSignalR_1.4.0.tgz |
| macOS Binary (sonoma-arm64) | BulkSignalR_1.4.0.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 |