README.md

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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 3.3.x 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, 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), .

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. , .

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

Testing

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



Bioconductor-mirror/derfinder documentation built on Aug. 8, 2017, 5:46 a.m.