derfinder

This package is for version 3.18 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: 3.18

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 "4.3") 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")

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 1.36.0

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/

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

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