Package: derfinderHelper 1.41.0
derfinderHelper: derfinder helper package
Helper package for speeding up the derfinder package when using multiple cores. This package is particularly useful when using BiocParallel and it helps reduce the time spent loading the full derfinder package when running the F-statistics calculation in parallel.
Authors:
derfinderHelper_1.41.0.tar.gz
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derfinderHelper_1.41.0.tgz(r-4.4-any)derfinderHelper_1.41.0.tgz(r-4.3-any)
derfinderHelper_1.41.0.tar.gz(r-4.5-noble)derfinderHelper_1.41.0.tar.gz(r-4.4-noble)
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derfinderHelper.pdf |derfinderHelper.html✨
derfinderHelper/json (API)
NEWS
# Install 'derfinderHelper' in R: |
install.packages('derfinderHelper', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/leekgroup/derfinderhelper/issues
On BioConductor:derfinderHelper-1.41.0(bioc 3.21)derfinderHelper-1.40.0(bioc 3.20)
differentialexpressionsequencingrnaseqsoftwareimmunooncologybioconductorderfinder
Last updated 19 days agofrom:4dbfb34928. Checks:OK: 7. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Dec 13 2024 |
R-4.5-win | OK | Dec 13 2024 |
R-4.5-linux | OK | Dec 13 2024 |
R-4.4-win | OK | Dec 13 2024 |
R-4.4-mac | OK | Dec 13 2024 |
R-4.3-win | OK | Dec 13 2024 |
R-4.3-mac | OK | Dec 13 2024 |
Exports:fstats.apply
Dependencies:BiocGenericsgenericsIRangeslatticeMatrixS4Vectors
Citation
Collado-Torres L, Jaffe AE, Leek JT (2017). derfinderHelper: derfinder helper package. doi:10.18129/B9.bioc.derfinderHelper, https://github.com/leekgroup/derfinderHelper - R package version 1.41.0, http://www.bioconductor.org/packages/derfinderHelper.
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, http://nar.oxfordjournals.org/content/early/2016/09/29/nar.gkw852.
Corresponding BibTeX entries:
@Manual{, title = {derfinderHelper: derfinder helper package}, author = {Leonardo Collado-Torres and Andrew E. Jaffe and Jeffrey T. Leek}, year = {2017}, url = {http://www.bioconductor.org/packages/derfinderHelper}, note = {https://github.com/leekgroup/derfinderHelper - R package version 1.41.0}, doi = {10.18129/B9.bioc.derfinderHelper}, }
@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}, }
Readme and manuals
derfinderHelper
Helper package for derfinder.
Documentation
For more information about derfinderHelper
check the vignettes
through Bioconductor
or at the documentation
website.
Installation instructions
Get the latest stable R
release from
CRAN. Then install derfinderHelper
from
Bioconductor using the following code:
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("derfinderHelper")
Citation
Below is the citation output from using citation('derfinderHelper')
in
R. Please run this yourself to check for any updates on how to cite
derfinderHelper.
print(citation("derfinderHelper"), bibtex = TRUE)
#> To cite package 'derfinderHelper' in publications use:
#>
#> Collado-Torres L, Jaffe AE, Leek JT (2017). _derfinderHelper:
#> derfinder helper package_. doi:10.18129/B9.bioc.derfinderHelper
#> <https://doi.org/10.18129/B9.bioc.derfinderHelper>,
#> https://github.com/leekgroup/derfinderHelper - R package version
#> 1.35.0, <http://www.bioconductor.org/packages/derfinderHelper>.
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Manual{,
#> title = {derfinderHelper: derfinder helper package},
#> author = {Leonardo Collado-Torres and Andrew E. Jaffe and Jeffrey T. Leek},
#> year = {2017},
#> url = {http://www.bioconductor.org/packages/derfinderHelper},
#> note = {https://github.com/leekgroup/derfinderHelper - R package version 1.35.0},
#> doi = {10.18129/B9.bioc.derfinderHelper},
#> }
#>
#> 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},
#> }
Please note that the derfinderHelper
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 derfinderHelper project is released with a Contributor 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 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.
Help Manual
Help page | Topics |
---|---|
Calculate F-statistics per base by extracting chunks from a DataFrame | fstats.apply |