Annotation-agnostic differential expression analysis of RNA-seq data via expressed regions-level or single base-level approaches
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R v1.15.2 -- fix IRanges subset method message Jul 24, 2018
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README.md

Status: Travis CI Build Status, Bioc-release , Bioc-devel .

Bioc-release , Bioc-devel , Codecov codecov.io

derfinder

Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach. This package contains two different implementations of this approach. The first one is the single base-level F-statistics implementation and the second one is via identifying expressed regions. For more information about derfinder check the vignettes here.

Further documentation

You can generate HTML reports from the results using regionReport available here.

Installation instructions

Get R 3.5.x from CRAN.

## From Bioconductor
install.packages("BiocManager")
BiocManager::install('derfinder')

## Suggested:
BiocManager::install(c('derfinderPlot', 'regionReport'))

Vignettes

The vignettes for this package can be viewed here or via Bioconductor's website.

'Watch' for updates

This software is in development, so we highly recommend 'watching' the repository: Click on the top right under Watch. You will then receive notifications for issues, comments, and pull requests as described here.

You will need a GitHub account to be able to Watch the repository.

Citation

Below is the citation output from using citation('derfinder') in R. Please run this yourself to check for any updates on how to cite derfinder.

To cite package derfinder in publications use:

Collado-Torres L, Nellore A, Frazee AC, Wilks C, Love MI, Langmead B, Irizarry RA, Leek JT and Jaffe AE (2016). “Flexible expressed region analysis for RNA-seq with derfinder.” Nucl. Acids Res.. doi: 10.1093/nar/gkw852 (URL: http://doi.org/10.1093/nar/gkw852), <URL: http://nar.oxfordjournals.org/content/early/2016/09/29/nar.gkw852>.

Frazee AC, Sabunciyan S, Hansen KD, Irizarry RA and Leek JT (2014). “Differential expression analysis of RNA-seq data at single-base resolution.” Biostatistics, 15 (3), pp. 413-426. <URL: http://dx.doi.org/10.1093/biostatistics/kxt053>, <URL: http://biostatistics.oxfordjournals.org/content/15/3/413.long>.

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 = {2016}, journal = {Nucl. Acids Res.}, doi = {10.1093/nar/gkw852}, url = {http://nar.oxfordjournals.org/content/early/2016/09/29/nar.gkw852}, }

@Article{, title = {Differential expression analysis of RNA-seq data at single-base resolution}, author = {Alyssa C. Frazee and Sarven Sabunciyan and Kasper D. Hansen and Rafael A. Irizarry and Jeffrey T. Leek}, year = {2014}, journal = {Biostatistics}, volume = {15 (3)}, pages = {413-426}, doi = {10.1093/biostatistics/kxt053}, url = {http://biostatistics.oxfordjournals.org/content/15/3/413.long}, }

DER Finder versions

  • The original implementation of the DER Finder approach as published in Frazee et al, Biostatistics 2014 is available via GitHub at derfinder.
  • The version implementing the single base-level approach via calculating F-stastics as described in the pre-print Collado-Torres et al, bioRxiv 2015 is available via Bioconductor at derfinder. The same package has the functions required for the expressed regions-level approach.

Testing

Testing on Bioc-devel is feasible thanks to R Travis as well as Bioconductor's nightly build.