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https://github.com/martaint/InterCellar


https://github.com/martaint/InterCellar

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README 

        
---

output: github_document

---



```{r, include = FALSE}

knitr::opts_chunk$set(

  collapse = TRUE,

  comment = "#>",

  fig.path = "man/figures/README-",

  out.width = "100%"

)

```



[![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 eval = FALSE}

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 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](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 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:

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 eval = FALSE}

library(InterCellar)

```



In order to start the app, please run the following command:



```{r demostart, eval=FALSE}

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 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 eval = FALSE}

BiocManager::install("ComplexHeatmap")

install.packages("golem")

```



And afterwards re-install `InterCellar`:



```{r eval = FALSE}

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 eval=FALSE}

Error in utils::browseURL(appUrl) : 

  'browser' must be a non-empty character string

```



Try this solution:



```{r eval=FALSE}

# 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 [[email protected]](mailto:[email protected])



## 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](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.