<!-- README.md is generated from README.Rmd. Please edit that file -->
# regionReport
<!-- badges: start -->
[](https://lifecycle.r-lib.org/articles/stages.html#stable)
[](https://bioconductor.org/checkResults/release/bioc-LATEST/regionReport)
[](https://bioconductor.org/checkResults/devel/bioc-LATEST/regionReport)
[](http://bioconductor.org/packages/stats/bioc/regionReport/)
[](https://support.bioconductor.org/tag/regionReport)
[](https://bioconductor.org/packages/release/bioc/html/regionReport.html#since)
[](http://bioconductor.org/checkResults/devel/bioc-LATEST/regionReport/)
[](https://bioconductor.org/packages/release/bioc/html/regionReport.html#since)
[](https://github.com/leekgroup/regionReport/actions)
[](https://github.com/leekgroup/regionReport/issues)
[](https://github.com/leekgroup/regionReport/pulls)
<!-- badges: end -->
Generate HTML reports for a set of regions such as those from
*[derfinder](https://bioconductor.org/packages/3.17/derfinder)* results
or any other pipeline that defines a set of genomic regions.
Check the documentation for `derfinderReport()` for an example on how to
create the necessary input files and generating the HTML report for
*[derfinder](https://bioconductor.org/packages/3.17/derfinder)* results.
Or use:
``` r
example("derfinderReport", "regionReport", ask = FALSE)
```
Similarly, check `renderReport()` for an example of a general report, or
use:
``` r
example("renderReport", "regionReport", ask = FALSE)
```
For *[DESeq2](https://bioconductor.org/packages/3.17/DESeq2)* or
*[edgeR](https://bioconductor.org/packages/3.17/edgeR)* results check
`DESeq2Report()` and `edgeReport()`.
## Documentation
For more information about `derfinderPlot` check the vignettes [through
Bioconductor](http://bioconductor.org/packages/regionReport) or at the
[documentation website](http://leekgroup.github.io/regionReport).
## Installation instructions
Get the latest stable `R` release from
[CRAN](http://cran.r-project.org/). Then install `regionReport` from
[Bioconductor](http://bioconductor.org/) using the following code:
``` r
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("regionReport")
```
## Citation
Below is the citation output from using `citation('regionReport')` in R.
Please run this yourself to check for any updates on how to cite
**regionReport**.
``` r
print(citation("regionReport"), bibtex = TRUE)
#> To cite package 'regionReport' in publications use:
#>
#> Collado-Torres L, Jaffe AE, Leek JT (2016). "regionReport:
#> Interactive reports for region-level and feature-level genomic
#> analyses [version2; referees: 2 approved, 1 approved with
#> reservations]." _F1000Research_, *4*, 105.
#> doi:10.12688/f1000research.6379.2
#> <https://doi.org/10.12688/f1000research.6379.2>,
#> <http://f1000research.com/articles/4-105/v2>.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Article{,
#> author = {Leonardo Collado-Torres and Andrew E. Jaffe and Jeffrey T. Leek},
#> title = {regionReport: Interactive reports for region-level and feature-level genomic analyses [version2; referees: 2 approved, 1 approved with reservations]},
#> journal = {F1000Research},
#> year = {2016},
#> doi = {10.12688/f1000research.6379.2},
#> url = {http://f1000research.com/articles/4-105/v2},
#> volume = {4},
#> pages = {105},
#> }
#>
#> Collado-Torres L, Nellore A, Frazee AC, Wilks C, Love MI, Langmead B,
#> Irizarry RA, Leek JT, Jaffe AE (2017). "Flexible expressed region
#> analysis for RNA-seq with derfinder." _Nucl. Acids Res._.
#> doi:10.1093/nar/gkw852 <https://doi.org/10.1093/nar/gkw852>,
#> <http://nar.oxfordjournals.org/content/early/2016/09/29/nar.gkw852>.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Article{,
#> title = {Flexible expressed region analysis for RNA-seq with derfinder},
#> author = {Leonardo Collado-Torres and Abhinav Nellore and Alyssa C. Frazee and Christopher Wilks and Michael I. Love and Ben Langmead and Rafael A. Irizarry and Jeffrey T. Leek and Andrew E. Jaffe},
#> year = {2017},
#> journal = {Nucl. Acids Res.},
#> doi = {10.1093/nar/gkw852},
#> url = {http://nar.oxfordjournals.org/content/early/2016/09/29/nar.gkw852},
#> }
#>
#> Collado-Torres L, Jaffe AE, Leek JT (2017). _regionReport: Generate
#> HTML or PDF reports for a set of genomic regions or DESeq2/edgeR
#> results_. doi:10.18129/B9.bioc.regionReport
#> <https://doi.org/10.18129/B9.bioc.regionReport>,
#> https://github.com/leekgroup/regionReport - R package version 1.35.0,
#> <http://www.bioconductor.org/packages/regionReport>.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Manual{,
#> title = {regionReport: Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results},
#> author = {Leonardo Collado-Torres and Andrew E. Jaffe and Jeffrey T. Leek},
#> year = {2017},
#> url = {http://www.bioconductor.org/packages/regionReport},
#> note = {https://github.com/leekgroup/regionReport - R package version 1.35.0},
#> doi = {10.18129/B9.bioc.regionReport},
#> }
```
Please note that the `regionReport` 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 regionReport 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.
## 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)*,
*[sysreqs](https://github.com/r-hub/sysreqs)* 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/3.17/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://leekgroup.github.io/derfinderPlot)
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/3.17/biocthis)*.
