Bioconductor – derfinder (development version)

DOI: 10.18129/B9.bioc.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 (3.15)

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
“4.2”) and enter:

if (!requireNamespace("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")

 

Details

biocViews ChIPSeq, Coverage, DifferentialExpression, DifferentialPeakCalling, ImmunoOncology, RNASeq, Sequencing, Software
Version 1.29.0
In Bioconductor since BioC 3.0 (R-3.1) (7 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
LinkingTo
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
SystemRequirements
Enhances
URL github.com/lcolladotor/derfinder
BugReports support.bioconductor.org/t/derfinder/
Depends On Me
Imports Me brainflowprobes, derfinderPlot, GenomicState, ODER, recount, recountWorkflow, regionReport
Suggests Me megadepth
Links To Me
Build Report  

Package Archives

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


Read more here: Source link