Generate HTML reports for a set of regions such as those from 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 results.
Or use:
example("derfinderReport", "regionReport", ask = FALSE)
Similarly, check renderReport()
for an example of a general report, or
use:
example("renderReport", "regionReport", ask = FALSE)
For DESeq2 or
edgeR results check
DESeq2Report()
and edgeReport()
.
For more information about derfinderPlot
check the vignettes through
Bioconductor or at the
documentation website.
Get the latest stable R
release from
CRAN. Then install regionReport
from
Bioconductor using the following code:
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("regionReport")
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.
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.
Please note that the regionReport project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.
- Continuous code testing is possible thanks to GitHub actions through usethis, remotes, sysreqs and rcmdcheck customized to use Bioconductor’s docker containers and BiocCheck.
- Code coverage assessment is possible thanks to codecov and covr.
- The documentation website is automatically updated thanks to pkgdown.
- The code is styled automatically thanks to styler.
- The documentation is formatted thanks to devtools and roxygen2.
For more details, check the dev
directory.
This package was developed using biocthis.