derfinder

This is the development version of derfinder; for the stable release version, see derfinder.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0

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

Bioconductor version: Development (3.24)

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] ORCID: 0000-0003-2140-308X , Alyssa C. Frazee [ctb], Andrew E. Jaffe [aut] ORCID: 0000-0001-6886-1454 , Jeffrey T. Leek [aut, ths] ORCID: 0000-0002-2873-2671

Maintainer: Leonardo Collado-Torres <lcolladotor at gmail.com>

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

Leonardo Collado-Torres, Andrew E. Jaffe, Jeffrey T. Leek. derfinder: Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach. doi:10.18129/B9.bioc.derfinder, R package version 1.47.0, https://bioconductor.org/packages/derfinder.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ChIPSeq, Coverage, DifferentialExpression, DifferentialPeakCalling, ImmunoOncology, RNASeq, Sequencing, Software
Version	1.47.0
In Bioconductor since	BioC 3.0 (R-3.1) (12 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), Seqinfo (>= 0.99.2), GenomeInfoDb (>= 1.45.9), GenomicAlignments, GenomicFeatures, GenomicFiles, GenomicRanges (>= 1.61.1), Hmisc, IRanges (>= 2.3.23), methods, qvalue (>= 1.99.0), Rsamtools (>= 2.25.1), rtracklayer, S4Vectors (>= 0.23.19), stats, utils
System Requirements
URL	https://github.com/lcolladotor/derfinder
Bug Reports	https://support.bioconductor.org/t/derfinder/

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
Linking To
Enhances
Depends On Me
Imports Me	derfinderPlot, GenomicState, recount, recountWorkflow, regionReport
Suggests Me	megadepth
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	derfinder_1.47.0.tar.gz
Windows Binary (x86_64)	derfinder_1.47.0.zip
macOS Binary (big-sur-x86_64)	derfinder_1.47.0.tgz
macOS Binary (sonoma-arm64)	derfinder_1.47.0.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