\[!\[Lifecycle: stable\](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)\](https://lifecycle.r-lib.org/articles/stages.html#stable) \[!\[install with bioconda\](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)\](http://bioconda.github.io/recipes/bioconductor-intercellar/README.html) # InterCellar 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 | |:--------------------------------------------------------------------------------:|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------:|:----------------------------------------------------------------------------:| | \[\*devel\*\](http://bioconductor.org/packages/devel/bioc/html/InterCellar.html) | \[!\[Bioconductor-devel Build Status\](http://bioconductor.org/shields/build/devel/bioc/InterCellar.svg)\](http://bioconductor.org/checkResults/devel/bioc-LATEST/InterCellar) | !\[\](http://bioconductor.org/shields/lastcommit/devel/bioc/InterCellar.svg) | | \[\*release\*\](http://bioconductor.org/packages/release/bioc/html/InterCellar.html) | \[!\[Bioconductor-release Build Status\](http://bioconductor.org/shields/build/release/bioc/InterCellar.svg)\](http://bioconductor.org/checkResults/release/bioc-LATEST/InterCellar) | !\[\](http://bioconductor.org/shields/lastcommit/release/bioc/InterCellar.svg) | ## Installation ### Bioconductor \`InterCellar\` is distributed as a \[Bioconductor\](https://www.bioconductor.org/) 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 \[Bioconda\](https://bioconda.github.io/recipes/bioconductor-intercellar/README.html). 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 \[here\](https://bioconda.github.io/recipes/bioconductor-intercellar/README.html). See \[bioconductor-intercellar/tags\](https://quay.io/repository/biocontainers/bioconductor-intercellar?tab=tags) for valid values for \\, then run: \`\`\` bash docker pull quay.io/biocontainers/bioconductor-intercellar: \`\`\` Lastly, you would need to run \`\`\` bash docker run -td quay.io/biocontainers/bioconductor-intercellar: docker exec -it /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 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: \`\`\` 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 \[here\](http://bioconductor.org/packages/devel/bioc/vignettes/InterCellar/inst/doc/user\_guide.html). ## Paper reproducibility Please have a look at \[InterCellar-reproducibility\](https://github.com/martaint/InterCellar-reproducibility) if you are interested in data and results showed in the \[manuscript\](https://www.researchsquare.com/article/rs-525466/v1). ## Help and Suggestions If you have any question, problem or suggestion, please feel free to open an \[issue\](https://github.com/martaint/InterCellar/issues) 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 \[Contributor Code of Conduct\](https://contributor-covenant.org/version/2/0/CODE\_OF\_CONDUCT.html). By contributing to this project, you agree to abide by its terms.
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 | |:--------------------------------------------------------------------------------:|:--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------:|:----------------------------------------------------------------------------:| | \[\*devel\*\](http://bioconductor.org/packages/devel/bioc/html/InterCellar.html) | \[!\[Bioconductor-devel Build Status\](http://bioconductor.org/shields/build/devel/bioc/InterCellar.svg)\](http://bioconductor.org/checkResults/devel/bioc-LATEST/InterCellar) | !\[\](http://bioconductor.org/shields/lastcommit/devel/bioc/InterCellar.svg) | | \[\*release\*\](http://bioconductor.org/packages/release/bioc/html/InterCellar.html) | \[!\[Bioconductor-release Build Status\](http://bioconductor.org/shields/build/release/bioc/InterCellar.svg)\](http://bioconductor.org/checkResults/release/bioc-LATEST/InterCellar) | !\[\](http://bioconductor.org/shields/lastcommit/release/bioc/InterCellar.svg) | ## Installation ### Bioconductor \`InterCellar\` is distributed as a \[Bioconductor\](https://www.bioconductor.org/) 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 \[Bioconda\](https://bioconda.github.io/recipes/bioconductor-intercellar/README.html). 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 \[here\](https://bioconda.github.io/recipes/bioconductor-intercellar/README.html). See \[bioconductor-intercellar/tags\](https://quay.io/repository/biocontainers/bioconductor-intercellar?tab=tags) for valid values for \\, then run: \`\`\` bash docker pull quay.io/biocontainers/bioconductor-intercellar: \`\`\` Lastly, you would need to run \`\`\` bash docker run -td quay.io/biocontainers/bioconductor-intercellar: docker exec -it /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 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: \`\`\` 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 \[here\](http://bioconductor.org/packages/devel/bioc/vignettes/InterCellar/inst/doc/user\_guide.html). ## Paper reproducibility Please have a look at \[InterCellar-reproducibility\](https://github.com/martaint/InterCellar-reproducibility) if you are interested in data and results showed in the \[manuscript\](https://www.researchsquare.com/article/rs-525466/v1). ## Help and Suggestions If you have any question, problem or suggestion, please feel free to open an \[issue\](https://github.com/martaint/InterCellar/issues) 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 \[Contributor Code of Conduct\](https://contributor-covenant.org/version/2/0/CODE\_OF\_CONDUCT.html). By contributing to this project, you agree to abide by its terms.