# iSEEde
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The goal of *[iSEEde](https://bioconductor.org/packages/iSEEde)* is
to provide panels that facilitate the interactive visualisation of
differential expression results in
*[iSEE](https://bioconductor.org/packages/iSEE)* applications.
## Installation instructions
Get the latest stable `R` release from
[CRAN](http://cran.r-project.org/). Then install
*[iSEEde](https://bioconductor.org/packages/iSEEde)* from
[Bioconductor](http://bioconductor.org/) using the following code:
``` r
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("iSEEde")
```
And the bleeding edge development version from
[GitHub](https://github.com/iSEE/iSEEde) with:
``` r
BiocManager::install("iSEE/iSEEde")
```
## Example
This is a basic example which shows you how to interactively explore
differential expression results for an example data set in an
*[iSEE](https://bioconductor.org/packages/iSEE)* application,
using designated panels implemented in
*[iSEEde](https://bioconductor.org/packages/iSEEde)*:
``` r
library("iSEEde")
library("airway")
library("DESeq2")
library("iSEE")
# Example data ----
data("airway")
airway$dex <- relevel(airway$dex, "untrt")
dds <- DESeqDataSet(airway, ~ 0 + dex + cell)
dds <- DESeq(dds)
res_deseq2 <- results(dds, contrast = list("dextrt", "dexuntrt"))
# iSEE / iSEEde ---
airway <- embedContrastResults(res_deseq2, airway, name = "dex: trt vs untrt")
app <- iSEE(airway, initial = list(
DETable(ContrastName="dex: trt vs untrt", HiddenColumns = c("baseMean",
"lfcSE", "stat"), PanelWidth = 4L),
VolcanoPlot(ContrastName="dex: trt vs untrt", PanelWidth = 4L),
MAPlot(ContrastName="dex: trt vs untrt", PanelWidth = 4L)
))
if (interactive()) {
shiny::runApp(app)
}
```
## Citation
Below is the citation output from using `citation('iSEEde')` in R.
Please run this yourself to check for any updates on how to cite
**iSEEde**.
``` r
print(citation("iSEEde"), bibtex = TRUE)
#>
#> To cite package 'iSEEde' in publications use:
#>
#> Rue-Albrecht K (2022). _iSEEde: iSEE extension for panels related to
#> differential expression analysis_. R package version 0.99.0,
#> <https://github.com/iSEE/iSEEde>.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Manual{,
#> title = {iSEEde: iSEE extension for panels related to differential expression analysis},
#> author = {Kevin Rue-Albrecht},
#> year = {2022},
#> note = {R package version 0.99.0},
#> url = {https://github.com/iSEE/iSEEde},
#> }
```
Please note that the
*[iSEEde](https://bioconductor.org/packages/iSEEde)* was only made
possible thanks to many other R and bioinformatics software authors,
which are cited either in the vignettes and/or the paper(s) describing
this package.
## Code of Conduct
Please note that the
*[iSEEde](https://bioconductor.org/packages/iSEEde)* project is
released with a [Contributor Code of
Conduct](http://bioconductor.org/about/code-of-conduct/). By
contributing to this project, you agree to abide by its terms.
## Development tools
- Continuous code testing is possible thanks to [GitHub
actions](https://www.tidyverse.org/blog/2020/04/usethis-1-6-0/)
through *[usethis](https://CRAN.R-project.org/package=usethis)*,
*[remotes](https://CRAN.R-project.org/package=remotes)*, and
*[rcmdcheck](https://CRAN.R-project.org/package=rcmdcheck)* customized
to use [Bioconductor’s docker
containers](https://www.bioconductor.org/help/docker/) and
*[BiocCheck](https://bioconductor.org/packages/BiocCheck)*.
- Code coverage assessment is possible thanks to
[codecov](https://codecov.io/gh) and
*[covr](https://CRAN.R-project.org/package=covr)*.
- The [documentation website](http://iSEE.github.io/iSEEde) is
automatically updated thanks to
*[pkgdown](https://CRAN.R-project.org/package=pkgdown)*.
- The code is styled automatically thanks to
*[styler](https://CRAN.R-project.org/package=styler)*.
- The documentation is formatted thanks to
*[devtools](https://CRAN.R-project.org/package=devtools)* and
*[roxygen2](https://CRAN.R-project.org/package=roxygen2)*.
For more details, check the `dev` directory.
This package was developed using
*[biocthis](https://bioconductor.org/packages/biocthis)*.
## Code of Conduct
Please note that the iSEEde project is released with a [Contributor Code
of Conduct](http://bioconductor.org/about/code-of-conduct/). By
contributing to this project, you agree to abide by its terms.
