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 (3.16)

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 "4.2") and enter:

if (!require("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	1.32.0
In Bioconductor since	BioC 3.0 (R-3.1) (8.5 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, ODER, 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_1.32.0.tar.gz
Windows Binary	derfinder_1.32.0.zip
macOS Binary (x86_64)	derfinder_1.32.0.tgz
macOS Binary (arm64)	derfinder_1.32.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/derfinder
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/derfinder
Bioc Package Browser	https://code.bioconductor.org/browse/derfinder/
Package Short Url	https://bioconductor.org/packages/derfinder/
Package Downloads Report	Download Stats