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To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("derfinder")
In most cases, you don't need to download the package archive at all.
derfinder
|
This package is for version 3.4 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: 3.4
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 <lcollado at jhu.edu>
Citation (from within R,
enter citation("derfinder")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("derfinder")
Documentation
| HTML | R Script | derfinder quick start guide |
| HTML | R Script | derfinder users guide |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | ChIPSeq, DifferentialExpression, DifferentialPeakCalling, RNASeq, Sequencing, Software |
| Version | 1.8.5 |
| In Bioconductor since | BioC 3.0 (R-3.1) (2.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.2) |
| Imports | AnnotationDbi(>= 1.27.9), BiocParallel, 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(>= 0.9.38) |
| LinkingTo | |
| Suggests | BiocStyle, biovizBase, devtools (>= 1.6), derfinderData(>= 0.99.0), derfinderPlot, DESeq2, ggplot2, knitcitations (>= 1.0.1), knitr (>= 1.6), limma, rmarkdown (>= 0.3.3), testthat, TxDb.Hsapiens.UCSC.hg19.knownGene |
| SystemRequirements | |
| Enhances | |
| URL | https://github.com/lcolladotor/derfinder |
| BugReports | https://support.bioconductor.org/t/derfinder/ |
| Depends On Me | |
| Imports Me | derfinderPlot, recount, regionReport |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | derfinder_1.8.5.tar.gz |
| Windows Binary | derfinder_1.8.5.zip |
| Mac OS X 10.9 (Mavericks) | derfinder_1.8.5.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/derfinder/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/derfinder/ |
| Package Downloads Report | Download Stats |
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