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 (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.46.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (12 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), Seqinfo(>= 0.99.2), GenomeInfoDb(>= 1.45.9), GenomicAlignments, GenomicFeatures, GenomicFiles, GenomicRanges(>= 1.61.1), Hmisc, IRanges(>= 2.3.23), methods, qvalue(>= 1.99.0), Rsamtools(>= 2.25.1), 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.
| Source Package | derfinder_1.46.0.tar.gz |
| Windows Binary (x86_64) | derfinder_1.46.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | derfinder_1.46.0.tgz |
| macOS Binary (sonoma-arm64) | derfinder_1.46.0.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 |