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<!-- README.md is generated from README.Rmd. Please edit that file --> <!-- badges: start --> <!-- badges: end -->InterCellar <img src="inst/app/www/logo_lowres.png" align="right" alt="" width="150" />
an R/Shiny app for interactive analysis and exploration of cell-cell communication based on single-cell transcriptomics data
Description
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.
Bioconductor release status
Branch | R CMD check | Last updated |
---|---|---|
devel | ||
release |
Installation
Bioconductor
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")
Bioconda and Docker
Alternatively, InterCellar
can be installed through
Bioconda.
We recommend installing InterCellar
in a fresh environment, such as:
conda create --name=intercellar_env
conda activate intercellar_env
conda install bioconductor-intercellar
Once the installation is done, you can start R simply by
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:
docker pull quay.io/biocontainers/bioconductor-intercellar:<tag>
Lastly, you would need to run
docker run -td quay.io/biocontainers/bioconductor-intercellar:<tag>
docker exec -it <container_ID> /bin/bash
R
Launching the app
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.
Troubleshooting
Bioconductor
It might happen that the installation through BiocManager
fails due to
missing packages, throwing a similar error:
ERROR: dependencies 'golem', 'ComplexHeatmap' are not available for package 'InterCellar'
One solution would be to install the missing packages independently, such as:
BiocManager::install("ComplexHeatmap")
install.packages("golem")
And afterwards re-install InterCellar
:
BiocManager::install("InterCellar")
Bioconda and Docker
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 )
User Guide
First time here? Please have a look at InterCellar
user guide
here.
Paper reproducibility
Please have a look at InterCellar-reproducibility if you are interested in data and results showed in the manuscript.
Help and Suggestions
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
Citation
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]
Code of Conduct
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.