derfinder

DOI: 10.18129/B9.bioc.derfinder    

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

Bioconductor version: Release (3.6)

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 [ctb], Andrew E. Jaffe [aut], Jeffrey T. Leek [aut, ths]

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

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	1.12.6
In Bioconductor since	BioC 3.0 (R-3.1) (3.5 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), methods, qvalue(>= 1.99.0), Rsamtools(>= 1.25.0), rtracklayer, S4Vectors(>= 0.9.38)
LinkingTo
Suggests	BiocStyle(>= 2.5.19), biovizBase, devtools (>= 1.6), derfinderData(>= 0.99.0), derfinderPlot, DESeq2, ggplot2, knitcitations (>= 1.0.1), knitr (>= 1.6), limma, RefManageR, rmarkdown (>= 0.3.3), testthat, TxDb.Hsapiens.UCSC.hg19.knownGene
SystemRequirements
Enhances
URL	https://github.com/lcolladotor/derfinder
BugReports	https://support.bioconductor.org/t/derfinder/
Depends On Me
Imports Me	derfinderPlot, recount, regionReport
Suggests Me
Build Report

Package Archives

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

Source Package	derfinder_1.12.6.tar.gz
Windows Binary	derfinder_1.12.6.zip
Mac OS X 10.11 (El Capitan)	derfinder_1.12.6.tgz
Source Repository	git clone https://git.bioconductor.org/packages/derfinder
Package Short Url	http://bioconductor.org/packages/derfinder/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive