alexg9010 / derfinder

Fast differential expression analysis of RNA-seq data at base-pair resolution

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

derfinder

Annotation-agnostic fast differential expression analysis of RNA-seq data at base-pair resolution. 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}, }

Testing

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

Origins

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.