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InterCellar: an R-Shiny app for interactive analysis and exploration of cell-cell communication in single-cell transcriptomics

Bioconductor version: Release (3.18)

InterCellar is implemented as an R/Bioconductor Package containing a Shiny app that allows users to interactively analyze cell-cell communication from scRNA-seq data. Starting from precomputed ligand-receptor interactions, InterCellar provides filtering options, annotations and multiple visualizations to explore clusters, genes and functions. Finally, based on functional annotation from Gene Ontology and pathway databases, InterCellar implements data-driven analyses to investigate cell-cell communication in one or multiple conditions.

Author: Marta Interlandi [cre, aut]

Maintainer: Marta Interlandi <marta.interlandi01 at gmail.com>

Citation (from within R, enter citation("InterCellar")):


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

InterCellar User Guide HTML R Script
Reference Manual PDF


biocViews GO, SingleCell, Software, Transcriptomics, Visualization
Version 2.8.0
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License MIT + file LICENSE
Depends R (>= 4.1)
Imports config, golem, shiny, DT, shinydashboard, shinyFiles, shinycssloaders, data.table, fs, dplyr, tidyr, circlize, colourpicker, dendextend, factoextra, ggplot2, plotly, plyr, shinyFeedback, shinyalert, tibble, umap, visNetwork, wordcloud2, readxl, htmlwidgets, colorspace, signal, scales, htmltools, ComplexHeatmap, grDevices, stats, tools, utils, biomaRt, rlang, fmsb, igraph
System Requirements
URL https://github.com/martaint/InterCellar
Bug Reports https://github.com/martaint/InterCellar/issues
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Suggests testthat (>= 3.0.0), knitr, rmarkdown, glue, graphite, processx, attempt, BiocStyle, httr
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package InterCellar_2.8.0.tar.gz
Windows Binary InterCellar_2.8.0.zip
macOS Binary (x86_64) InterCellar_2.8.0.tgz
macOS Binary (arm64) InterCellar_2.8.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/InterCellar
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/InterCellar
Bioc Package Browser https://code.bioconductor.org/browse/InterCellar/
Package Short Url https://bioconductor.org/packages/InterCellar/
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