Package: derfinderHelper 1.41.0

Leonardo Collado-Torres

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:Leonardo Collado-Torres [aut, cre], Andrew E. Jaffe [aut], Jeffrey T. Leek [aut, ths]

derfinderHelper_1.41.0.tar.gz
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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'))

Peer review:

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

6.20 score 7 packages 864 downloads 1 exports 6 dependencies

Last updated 19 days agofrom:4dbfb34928. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 13 2024
R-4.5-winOKDec 13 2024
R-4.5-linuxOKDec 13 2024
R-4.4-winOKDec 13 2024
R-4.4-macOKDec 13 2024
R-4.3-winOKDec 13 2024
R-4.3-macOKDec 13 2024

Exports:fstats.apply

Dependencies:BiocGenericsgenericsIRangeslatticeMatrixS4Vectors

Introduction to derfinderHelper

Rendered fromderfinderHelper.Rmdusingknitr::rmarkdownon Dec 13 2024.

Last update: 2024-12-12
Started: 2014-09-23

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

For more details, check the dev directory.