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

derfinder

Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution by calculating F-statistics. 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 3.2.0 from CRAN.

## From Bioconductor
source('http://bioconductor.org/biocLite.R')
biocLite('derfinder')

## Suggested:
biocLite(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, Frazee AC, Love MI, Irizarry RA, Jaffe AE and Leek JT (2015). "derfinder: Software for annotation-agnostic RNA-seq differential expression analysis". bioRxiv. <URL: http://dx.doi.org/10.1101/015370>, <URL: http://www.biorxiv.org/content/early/2015/02/19/015370.abstract>.

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

@Manual{, title = {derfinder: Software for annotation-agnostic RNA-seq differential expression analysis}, author = {Leonardo Collado-Torres and Alyssa C. Frazee and Michael I. Love and Rafael A. Irizarry and Andrew E. Jaffe and Jeffrey T. Leek}, year = {2015}, journal = {bioRxiv}, doi = {10.1101/015370}, url = {http://www.biorxiv.org/content/early/2015/02/19/015370.abstract} }

@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 approach via calculating F-stastics as described in the pre-print Collado-Torres et al, bioRxiv 2015 is available via Bioconductor at derfinder.
• The version implementing the expressed-regions approach is available via GitHub at derfinder2. In the future it will also be available via Bioconductor.

Testing

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