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.
This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see derfinder.
Bioconductor version: 3.3
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 [aut], Andrew E. Jaffe [aut], Jeffrey T. Leek [aut, ths]
Maintainer: Leonardo Collado-Torres <lcollado at jhu.edu>
Citation (from within R,
enter citation("derfinder")
):
To install this package, start R and enter:
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("derfinder")
HTML | R Script | derfinder quick start guide |
HTML | R Script | derfinder users guide |
Reference Manual | ||
Text | NEWS |
biocViews | ChIPSeq, DifferentialExpression, DifferentialPeakCalling, RNASeq, Sequencing, Software |
Version | 1.6.4 |
In Bioconductor since | BioC 3.0 (R-3.1) (2 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), qvalue(>= 1.99.0), Rsamtools, 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://github.com/lcolladotor/derfinder/issues |
Depends On Me | |
Imports Me | derfinderPlot, regionReport |
Suggests Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Package Source | derfinder_1.6.4.tar.gz |
Windows Binary | derfinder_1.6.4.zip |
Mac OS X 10.9 (Mavericks) | derfinder_1.6.4.tgz |
Subversion source | (username/password: readonly) |
Git source | https://github.com/Bioconductor-mirror/derfinder/tree/release-3.3 |
Package Short Url | http://bioconductor.org/packages/derfinder/ |
Package Downloads Report | Download Stats |
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