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<!-- is generated from README.Rmd. Please edit that file --> <!-- badges: start --> [![Lifecycle: stable](]( [![install with bioconda](]( <!-- 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*]( | [![Bioconductor-devel Build Status](]( | ![]( | | [*release*]( | [![Bioconductor-release Build Status](]( | ![]( | ## 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: ``` r 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: ``` bash 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 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 docker pull<tag> ``` Lastly, you would need to run ``` bash docker run -td<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: ``` r library(InterCellar) ``` In order to start the app, please run the following command: ``` r 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`). 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: ``` bash 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`: ``` r 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: ``` r Error in utils::browseURL(appUrl) : 'browser' must be a non-empty character string ``` Try this solution: ``` r # 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 <> ## 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). \[<>\] ## 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.