Status: Travis CI , Bioc-release , Bioc-devel .
Bioc-release , Bioc-devel , Codecov
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 3.2.0 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, Nellore A, Frazee AC, Wilks C, Love MI, Irizarry RA, Leek JT and Jaffe AE (2016). "Flexible expressed region analysis for RNA-seq with derfinder". bioRxiv. <URL: http://dx.doi.org/10.1101/015370>, <URL: http://biorxiv.org/content/early/2016/05/07/015370>.
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 = {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 Rafael A. Irizarry and Jeffrey T. Leek and Andrew E. Jaffe}, year = {2016}, journal = {bioRxiv}, doi = {10.1101/015370}, url = {http://biorxiv.org/content/early/2016/05/07/015370} }
@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-level approach via calculating F-stastics as described in the pre-print Collado-Torres et al, bioRxiv 2015 is available via Bioconductor at derfinder. The same package has the functions required for the expressed regions-level approach.
Testing
Testing on Bioc-devel is feasible thanks to R Travis as well as Bioconductor's nightly build.