Status: Travis CI 
Annotation-agnostic fast differential expression analysis of RNA-seq data at base-pair resolution. For more information about derfinder check the vignettes here.
You can generate HTML reports from the results using regionReport available here.
Get R 3.2.0 from CRAN.
## From Bioconductor
source('http://bioconductor.org/biocLite.R')
biocLite('derfinder')
## Suggested:
biocLite(c('derfinderPlot', 'regionReport'))The vignettes for this package can be viewed here or via Bioconductor's website.
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.
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}, }
Testing on Bioc-devel is feasible thanks to r-builder as well as Bioconductor's nightly build.
This is a development version for a faster version of the derfinder core steps. The original implementation is available via GitHub at the derfinder repository.