knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.path = "man/figures/README-", out.width = "100%" )
an R/Shiny app for interactive analysis and exploration of cell-cell communication based on single-cell transcriptomics data
InterCellar
allows researchers to interactively analyze the results
of cell-cell communication from scRNA-seq data. Starting from pre-computed ligand-receptor
interactions, InterCellar
provides filtering options, annotations and multiple visualizations
to explore clusters, genes and functions. Moreover, 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.
Every step of the analysis can be
performed interactively, thus not requiring any programming skills. Moreover,
InterCellar
runs on your local machine, avoiding issues related to data privacy.
| Branch | R CMD check | Last updated |
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| devel | |
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| release |
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InterCellar
is distributed as a Bioconductor package and requires R (version 4.1) and Bioconductor (version 3.14).
To install InterCellar
package enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("InterCellar")
Alternatively, InterCellar
can be installed through Bioconda. We recommend installing InterCellar
in a fresh environment, such as:
```{bash eval = FALSE} conda create --name=intercellar_env conda activate intercellar_env conda install bioconductor-intercellar
Once the installation is done, you can start R simply by ```{bash eval = FALSE} R
A third option would be to pull the docker container as indicated here. See bioconductor-intercellar/tags for valid values for \<tag>, then run:
```{bash eval = FALSE}
docker pull quay.io/biocontainers/bioconductor-intercellar:
Lastly, you would need to run ```{bash eval = FALSE} docker run -td quay.io/biocontainers/bioconductor-intercellar:<tag> docker exec -it <container_ID> /bin/bash R
Once InterCellar
is successfully installed, it can be loaded inside R or Rstudio as follow:
library(InterCellar)
In order to start the app, please run the following command:
InterCellar::run_app( reproducible = TRUE )
InterCellar
should be opening in a browser. If this does not happen automatically,
please open a browser and navigate to the address shown (for example, Listening on http://127.0.0.1:6134
). The flag reproducible = TRUE
ensures that your results will
be reproducible across R sessions.
It might happen that the installation through BiocManager
fails due to missing packages, throwing a similar error:
```{bash eval = FALSE} ERROR: dependencies 'golem', 'ComplexHeatmap' are not available for package 'InterCellar'
One solution would be to install the missing packages independently, such as: ```r BiocManager::install("ComplexHeatmap") install.packages("golem")
And afterwards re-install InterCellar
:
BiocManager::install("InterCellar")
For users that have installed InterCellar
through Bioconda or Docker, running InterCellar::run_app()
might fail due to this error:
Error in utils::browseURL(appUrl) : 'browser' must be a non-empty character string
Try this solution:
# After starting R options(browser="firefox") # and then as usual InterCellar::run_app( reproducible = TRUE )
First time here? Please have a look at InterCellar
user guide here.
Please have a look at InterCellar-reproducibility if you are interested in data and results showed in the manuscript.
If you have any question, problem or suggestion, please feel free to open an issue or contact Marta Interlandi at marta.interlandi@uni-muenster.de
Interlandi, M., Kerl, K. & Dugas, M. InterCellar enables interactive analysis and exploration of cell−cell communication in single-cell transcriptomic data. Commun Biol 5, 21 (2022). [https://doi.org/10.1038/s42003-021-02986-2]
Please note that the InterCellar project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.
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