Package: SingleCellSignalR 2.3.0

Jean-Philippe Villemin

SingleCellSignalR: Cell Signalling Using Single-Cell RNA-seq or Proteomics Data

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.

Authors:Jacques Colinge [aut], Jean-Philippe Villemin [cre]

SingleCellSignalR_2.3.0.tar.gz
SingleCellSignalR_2.3.0.zip(r-4.7)SingleCellSignalR_2.3.0.zip(r-4.6)SingleCellSignalR_2.3.0.zip(r-4.5)
SingleCellSignalR_2.3.0.tgz(r-4.6-any)SingleCellSignalR_2.3.0.tgz(r-4.5-any)
SingleCellSignalR_2.3.0.tar.gz(r-4.7-any)SingleCellSignalR_2.3.0.tar.gz(r-4.6-any)
SingleCellSignalR_2.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SingleCellSignalR/json (API)

# Install 'SingleCellSignalR' in R:

install.packages('SingleCellSignalR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jcolinge/singlecellsignalr/issues

Datasets:

example_dataset - An example of single-cell RNA-seq data set

On BioConductor:SingleCellSignalR-2.3.0(bioc 3.24)SingleCellSignalR-2.2.0(bioc 3.23)

network rnaseq software proteomics transcriptomics singlecell networkinference

6.50 score 1 stars 43 scripts 7 mentions 12 exports 193 dependencies

Last updated from:8b72731b79. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	259
linux-devel-x86_64	OK	474
source / vignettes	OK	339
linux-release-x86_64	OK	461
macos-release-arm64	OK	307
macos-oldrel-arm64	OK	246
windows-devel	OK	375
windows-release	OK	353
windows-oldrel	OK	336
wasm-release	OK	238

Exports:autocrines bsrdmComp cellNetBubblePlot cellNetHeatmap getAutocrines getParacrines infParamSC paracrines performInferences populations SCSRNet SCSRNoNet

Dependencies:abind ape aplot askpass babelgene backports base64enc Biobase BiocFileCache BiocGenerics bit bit64 bitops blob boot broom bslib BulkSignalR cachem car carData circlize cli clipr clue cluster codetools colorspace ComplexHeatmap corrplot cowplot cpp11 crayon crosstalk curl data.table DBI dbplyr DelayedArray Deriv digest doBy doParallel dplyr evaluate farver fastmap filelock fontawesome fontBitstreamVera fontLiberation fontquiver foreach forecast Formula fracdiff fs gdtools generics GenomicRanges GetoptLong ggalluvial ggfun ggiraph ggplot2 ggplotify ggpubr ggrepel ggsci ggsignif ggtree glmnet GlobalOptions glue gprofiler2 gridExtra gridGraphics gtable highr hms homologene htmltools htmlwidgets httr httr2 igraph IRanges isoband iterators jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle lme4 lmtest magick magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats matrixTests memoise mgcv mime minqa modelr multtest nlme nloptr nnet numDeriv openssl orthogene otel patchwork pbkrtest pillar pkgconfig plotly plyr png polynom prettyunits progress promises purrr quantreg R.cache R.methodsS3 R.oo R.utils R6 RANN rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl Rdpack readr reformulas repmis rjson rlang rmarkdown RSQLite rstatix Rtsne S4Arrays S4Vectors S7 sass scales Seqinfo shape SingleCellExperiment SparseArray SparseM SpatialExperiment stabledist stringi stringr SummarizedExperiment survival sys systemfonts tibble tidyr tidyselect tidytree timeDate tinytex treeio tzdb urca utf8 vctrs viridisLite vroom withr xfun XVector yaml yulab.utils zoo

SingleCellSignalR : Inference of ligand-receptor interactions from single-cell data

What is it for? | Main worfklow | Acknowledgements | Session Information

Rendered fromSingleCellSignalR-Main.Rmdusingknitr::rmarkdown

Last update: 2026-04-16
Started: 2025-09-28

Help page	Topics
autocrines accessor	autocrines autocrines,SCSRNet-method autocrines,SCSRNoNet-method
BSRDataModelComp object accessor	bsrdmComp bsrdmComp,SCSRNet-method bsrdmComp,SCSRNoNet-method
Overview of cellular networks with a bubble plot	cellNetBubblePlot
Heatmap overview of cellular networks	cellNetHeatmap
An example of single-cell RNA-seq data set	example_dataset
Method to retrieve autocrine interactions	getAutocrines getAutocrines,SCSRNet-method getAutocrines,SCSRNoNet-method
Method to retrieve paracrine interactions	getParacrines getParacrines,SCSRNet-method getParacrines,SCSRNoNet-method
Inference parameters accessor	infParamSC infParamSC,SCSRNet-method infParamSC,SCSRNoNet-method
paracrines accessor	paracrines paracrines,SCSRNet-method paracrines,SCSRNoNet-method
Inference of ligand-receptor interactions based on regulation	performInferences performInferences,SCSRNet-method performInferences,SCSRNoNet-method
populations accessor	populations populations,SCSRNet-method populations,SCSRNoNet-method
Instantiate a SCSRNet object from expression data	SCSRNet
SingleCellSignalR cellular network object	SCSRNet-class
Prepare a SCSRNoNet object from expression data	SCSRNoNet
SingleCellSignalR no network object	SCSRNoNet-class

Package: SingleCellSignalR 2.3.0

SingleCellSignalR: Cell Signalling Using Single-Cell RNA-seq or Proteomics Data

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