derfinder
This is the released version of derfinder; for the devel version, see derfinder.
All Bioconductor versions of derfinder
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: 3.23 · Package version: 1.46.0
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"):
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 1.46.0, 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")
BiocManager::install("derfinder")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.46.0 |
| License | Artistic-2.0 |
| URL | https://github.com/lcolladotor/derfinder |
| Bug Reports | https://support.bioconductor.org/t/derfinder/ |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.0 (R-3.1) (11 years) |
| Downloads rank | 296 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | ChIPSeq, Coverage, DifferentialExpression, DifferentialPeakCalling, ImmunoOncology, RNASeq, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/derfinder/ |
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 | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | derfinder_1.46.0.tar.gz |
| Windows binary (x86_64) | derfinder_1.46.0.zip |
| macOS binary (arm64) | derfinder_1.46.0.tgz |
| macOS binary (x86_64) | derfinder_1.46.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/derfinder |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/derfinder |
| Package Downloads Report | Download Stats |
Dependencies
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
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
Reverse dependencies
Imports Me (5): derfinderPlot, GenomicState, recount, recountWorkflow, regionReport
Suggests Me (1): megadepth