derfinder
This package is for version 3.17 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: 3.17
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("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 | ||
| NEWS | Text |
Details
| biocViews | ChIPSeq, Coverage, DifferentialExpression, DifferentialPeakCalling, ImmunoOncology, RNASeq, Sequencing, Software |
| Version | 1.34.0 |
| 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/ |
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 | brainflowprobes, derfinderPlot, GenomicState, ODER, recount, recountWorkflow, regionReport |
| Suggests Me | megadepth |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | derfinder_1.34.0.tar.gz |
| Windows Binary | derfinder_1.34.0.zip |
| macOS Binary (x86_64) | derfinder_1.34.0.tgz |
| macOS Binary (arm64) | derfinder_1.34.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/derfinder |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/derfinder |
| Bioc Package Browser | https://code.bioconductor.org/browse/derfinder/ |
| Package Short Url | https://bioconductor.org/packages/derfinder/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.17 | Source Archive |