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This package is for version 3.2 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: 3.2

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) identification of expressed-regions.

Author: Leonardo Collado-Torres [aut, cre], Alyssa C. Frazee [aut], Andrew E. Jaffe [aut], Jeffrey T. Leek [aut, ths]

Maintainer: Leonardo Collado-Torres <lcollado at>

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biocViews DifferentialExpression, RNASeq, Sequencing, Software
Version 1.4.4
In Bioconductor since BioC 3.0 (R-3.1) (1.5 years)
License Artistic-2.0
Depends R (>= 3.2)
Imports AnnotationDbi(>= 1.27.9), BiocParallel, bumphunter(>= 1.9.2), derfinderHelper(>= 1.1.0), GenomeInfoDb(>= 1.3.3), GenomicAlignments, GenomicFeatures, GenomicFiles, GenomicRanges(>= 1.17.40), Hmisc, IRanges(>= 2.3.23), qvalue(>= 1.99.0), Rsamtools, rtracklayer, S4Vectors(>= 0.7.20)
Suggests BiocStyle, biovizBase, devtools (>= 1.6), derfinderData(>= 0.99.0), ggplot2, knitcitations (>= 1.0.1), knitr (>= 1.6), rmarkdown (>= 0.3.3), testthat, TxDb.Hsapiens.UCSC.hg19.knownGene
Depends On Me
Imports Me derfinderPlot, regionReport
Suggests Me
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