SingleCellSignalR
This is the released version of SingleCellSignalR; for the devel version, see SingleCellSignalR.
Cell Signalling Using Single-Cell RNA-seq or Proteomics Data
Bioconductor version: Release (3.23)
Inference of ligand-receptor (L-R) interactions from single-cell expression (transcriptomics/proteomics) data. SingleCellSignalR v2 inferences rely on the statistical model we introduced in the BulkSignalR package as well as the original SingleCellSignalR LR-score (both are available). SingleCellSignalR v2 can be regarded as a wrapper to BulkSignalR fundamental classes. This also enables v2 users to work with any species, whereas only Mus musculus & Homo sapiens were available before in SingleCellSignalR v1.
Author: Jacques Colinge [aut]
, Jean-Philippe Villemin [cre]
Maintainer: Jean-Philippe Villemin <jpvillemin at gmail.com>
citation("SingleCellSignalR")):
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("SingleCellSignalR")
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("SingleCellSignalR")| SingleCellSignalR-Main | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Network, NetworkInference, Proteomics, RNASeq, SingleCell, Software, Transcriptomics |
| Version | 2.2.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (6.5 years) |
| License | CeCILL | file LICENSE |
| Depends | R (>= 4.5) |
| Imports | stats, utils, methods, ggplot2, matrixTests, matrixStats, foreach, BulkSignalR, grid, ComplexHeatmap, circlize |
| System Requirements | |
| URL | https://github.com/jcolinge/SingleCellSignalR |
| Bug Reports | https://github.com/jcolinge/SingleCellSignalR/issues |
See More
| Suggests | knitr, markdown, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | tidySingleCellExperiment |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SingleCellSignalR_2.2.0.tar.gz |
| Windows Binary (x86_64) | SingleCellSignalR_2.2.0.zip |
| macOS Binary (big-sur-x86_64) | SingleCellSignalR_2.2.0.tgz |
| macOS Binary (sonoma-arm64) | SingleCellSignalR_2.2.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SingleCellSignalR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SingleCellSignalR |
| Bioc Package Browser | https://code.bioconductor.org/browse/SingleCellSignalR/ |
| Package Short Url | https://bioconductor.org/packages/SingleCellSignalR/ |
| Package Downloads Report | Download Stats |