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https://github.com/martaint/InterCellar
https://github.com/martaint/InterCellar
Last synced: 4 months ago
JSON representation
- Host: GitHub
- URL: https://github.com/martaint/InterCellar
- Owner: martaint
- License: other
- Created: 2021-01-04T18:39:13.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2022-04-06T08:47:55.000Z (about 2 years ago)
- Last Synced: 2024-02-14T22:23:05.161Z (4 months ago)
- Language: R
- Size: 11.3 MB
- Stars: 8
- Watchers: 2
- Forks: 4
- Open Issues: 1
-
Metadata Files:
- Readme: README.Rmd
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
Lists
- awesome-single-cell - InterCellar - [R] - an R/Shiny app for interactive analysis and exploration of cell-cell communication based on single-cell transcriptomics data. Starting from pre-computed ligand-receptor interactions, InterCellar provides filtering options, annotations and multiple visualizations to explore cell 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. ([Interlandi et al. 2022](https://doi.org/10.1038/s42003-021-02986-2)). (Web portals, apps, and databases / Interactive visualization and analysis)
- awesome-cell-cell-communication - InterCellar - [R]- InterCellar is an R/Shiny app for interactive analysis and exploration of cell-cell communication based on single-cell transcriptomics data. (Uncategorized / Uncategorized)
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/bashR
```## 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.