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

This package is for version 3.1 of Bioconductor; for the stable, up-to-date release version, see derfinder.

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

Bioconductor version: 3.1

This package provides functions for annotation-agnostic differential expression analysis of RNA-seq data.

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")):

To install this package, start R and enter:

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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("derfinder")

HTML	R Script	derfinder advanced details and usage
HTML	R Script	Introduction to derfinder
PDF		Reference Manual
Text		NEWS

biocViews	DifferentialExpression, RNASeq, Sequencing, Software
Version	1.2.1
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(>= 1.7.6), derfinderHelper(>= 1.1.0), GenomeInfoDb(>= 1.3.3), GenomicAlignments, GenomicFeatures, GenomicFiles, GenomicRanges(>= 1.17.40), Hmisc, IRanges(>= 1.99.28), qvalue(>= 1.99.0), Rsamtools, rtracklayer, S4Vectors(>= 0.2.3)
LinkingTo
Suggests	biovizBase, devtools (>= 1.6), derfinderData(>= 0.99.0), ggplot2, knitcitations (>= 1.0.1), knitr (>= 1.6), knitrBootstrap (>= 0.9.0), 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

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

Package Source	derfinder_1.2.1.tar.gz
Windows Binary	derfinder_1.2.1.zip
Mac OS X 10.6 (Snow Leopard)	derfinder_1.2.1.tgz
Mac OS X 10.9 (Mavericks)	derfinder_1.2.1.tgz
Subversion source	(username/password: readonly)
Git source	https://github.com/Bioconductor-mirror/derfinder/tree/release-3.1
Package Short Url	http://bioconductor.org/packages/derfinder/
Package Downloads Report	Download Stats

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