To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("derfinder")

In most cases, you don't need to download the package archive at all.

derfinder

 

   

Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach

Bioconductor version: Release (3.3)

This package provides functions for annotation-agnostic differential expression analysis of RNA-seq data. Two implementations of the DER Finder approach are included in this package: (1) single base-level F-statistics and (2) DER identification at the expressed regions-level. The DER Finder approach can also be used to identify differentially bounded ChIP-seq peaks.

Author: Leonardo Collado-Torres [aut, cre], Alyssa C. Frazee [aut], Andrew E. Jaffe [aut], Jeffrey T. Leek [aut, ths]

Maintainer: Leonardo Collado-Torres <lcollado at jhu.edu>

Citation (from within R, enter citation("derfinder")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("derfinder")

Documentation

HTML R Script derfinder quick start guide
HTML R Script derfinder users guide
PDF   Reference Manual
Text   NEWS

Details

biocViews ChIPSeq, DifferentialExpression, DifferentialPeakCalling, RNASeq, Sequencing, Software
Version 1.6.4
In Bioconductor since BioC 3.0 (R-3.1) (1.5 years)
License Artistic-2.0
Depends R (>= 3.2)
Imports AnnotationDbi(>= 1.27.9), BiocParallel, bumphunter(>= 1.9.2), derfinderHelper(>= 1.1.0), GenomeInfoDb(>= 1.3.3), GenomicAlignments, GenomicFeatures, GenomicFiles, GenomicRanges(>= 1.17.40), Hmisc, IRanges(>= 2.3.23), qvalue(>= 1.99.0), Rsamtools, rtracklayer, S4Vectors(>= 0.9.38)
LinkingTo
Suggests BiocStyle, biovizBase, devtools (>= 1.6), derfinderData(>= 0.99.0), derfinderPlot, DESeq2, ggplot2, knitcitations (>= 1.0.1), knitr (>= 1.6), limma, rmarkdown (>= 0.3.3), testthat, TxDb.Hsapiens.UCSC.hg19.knownGene
SystemRequirements
Enhances
URL https://github.com/lcolladotor/derfinder
BugReports https://github.com/lcolladotor/derfinder/issues
Depends On Me
Imports Me derfinderPlot, regionReport
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source derfinder_1.6.4.tar.gz
Windows Binary derfinder_1.6.4.zip
Mac OS X 10.9 (Mavericks) derfinder_1.6.4.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/derfinder/tree/release-3.3
Package Short Url http://bioconductor.org/packages/derfinder/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: