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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
<!-- badges: start -->
[](https://lifecycle.r-lib.org/articles/stages.html#stable)
[](http://bioconda.github.io/recipes/bioconductor-intercellar/README.html)
<!-- 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_](http://bioconductor.org/packages/devel/bioc/html/InterCellar.html) | [](http://bioconductor.org/checkResults/devel/bioc-LATEST/InterCellar) |  |
| [_release_](http://bioconductor.org/packages/release/bioc/html/InterCellar.html) | [](http://bioconductor.org/checkResults/release/bioc-LATEST/InterCellar) |  |
## 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 \<tag\>, then run:
```{bash eval = FALSE}
docker pull quay.io/biocontainers/bioconductor-intercellar:<tag>
```
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
```
## 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.