derfinder

DOI: 10.18129/B9.bioc.derfinder    

This package is for version 3.12 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 via the DER Finder approach

Bioconductor version: 3.12

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 <lcolladotor at gmail.com>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("derfinder")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("derfinder")

 

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

Details

biocViews	ChIPSeq, Coverage, DifferentialExpression, DifferentialPeakCalling, ImmunoOncology, RNASeq, Sequencing, Software
Version	1.24.2
In Bioconductor since	BioC 3.0 (R-3.1) (6.5 years)
License	Artistic-2.0
Depends	R (>= 3.5.0)
Imports	BiocGenerics(>= 0.25.1), AnnotationDbi(>= 1.27.9), BiocParallel(>= 1.15.15), 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(>= 0.23.19), stats, utils
LinkingTo
Suggests	BiocStyle(>= 2.5.19), sessioninfo, derfinderData(>= 0.99.0), derfinderPlot, DESeq2, ggplot2, knitr (>= 1.6), limma, RefManageR, rmarkdown (>= 0.3.3), testthat (>= 2.1.0), TxDb.Hsapiens.UCSC.hg19.knownGene, covr
SystemRequirements
Enhances
URL	https://github.com/lcolladotor/derfinder
BugReports	https://support.bioconductor.org/t/derfinder/
Depends On Me
Imports Me	brainflowprobes, derfinderPlot, GenomicState, recount, recountWorkflow, regionReport
Suggests Me	megadepth
Links To Me
Build Report

Package Archives

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

Source Package	derfinder_1.24.2.tar.gz
Windows Binary	derfinder_1.24.2.zip
macOS 10.13 (High Sierra)	derfinder_1.24.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/derfinder
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/derfinder
Package Short Url	https://bioconductor.org/packages/derfinder/
Package Downloads Report	Download Stats