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Bioconductor - derfinder

derfinder

This is the released version of derfinder; for the devel version, see derfinder.

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

Bioconductor version: Release (3.21)

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")): Installation

To install this package, start R (version "4.5") 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")

Details biocViews ChIPSeq, Coverage, DifferentialExpression, DifferentialPeakCalling, ImmunoOncology, RNASeq, Sequencing, Software Version 1.42.0 In Bioconductor since BioC 3.0 (R-3.1) (10.5 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 derfinderPlot, recount, regionReport, GenomicState, recountWorkflow Suggests Me megadepth Links To Me Build Report Build Report Package Archives

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

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