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.

For a full example on how to use derfinder check derfinderExample. TODO: update this.

Installation instructions

Get R 3.1.1 or newer 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, Jaffe AE and Leek JT (2014). derfinder: Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution. https://github.com/lcolladotor/derfinder - R package version 1.1.15, <URL: http://www.bioconductor.org/packages/release/bioc/html/derfinder.html>.

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: Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution}, author = {Leonardo Collado-Torres and Alyssa C. Frazee and Andrew E. Jaffe and Jeffrey T. Leek}, year = {2014}, url = {http://www.bioconductor.org/packages/release/bioc/html/derfinder.html}, note = {https://github.com/lcolladotor/derfinder - R package version 1.1.15}, }

@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}, }

Travis CI

This package is automatically tested thanks to Travis CI and r-travis. If you want to add this to your own package use:

## Use devtools to create the .travis.yml file
library('devtools')
use_travis('yourPackage')

## Read https://github.com/craigcitro/r-travis/wiki to configure .travis.yml appropriately

## Add a status image by following the info at http://docs.travis-ci.com/user/status-images/

Testing on R-devel for Bioc-devel is feasible thanks to r-builder.

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.