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derfinder

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

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


Bioconductor version: Development (3.19)

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>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
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

Details

biocViews ChIPSeq, Coverage, DifferentialExpression, DifferentialPeakCalling, ImmunoOncology, RNASeq, Sequencing, Software
Version 1.37.0
In Bioconductor since BioC 3.0 (R-3.1) (9.5 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
System Requirements
URL https://github.com/lcolladotor/derfinder
Bug Reports https://support.bioconductor.org/t/derfinder/
See More
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 brainflowprobes, derfinderPlot, GenomicState, recount, recountWorkflow, regionReport
Suggests Me megadepth
Links To Me
Build Report Build Report

Package Archives

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

Source Package derfinder_1.37.0.tar.gz
Windows Binary derfinder_1.37.0.zip
macOS Binary (x86_64) derfinder_1.37.0.tgz
macOS Binary (arm64)
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