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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
|
Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach
Bioconductor version: 3.2
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) identification of expressed-regions.
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")):
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
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("derfinder")
| HTML | derfinder advanced details and usage | |
| HTML | Introduction to derfinder | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DifferentialExpression, RNASeq, Sequencing, Software |
| Version | 1.4.4 |
| In Bioconductor since | BioC 3.0 (R-3.1) (1.5 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), qvalue(>= 1.99.0), Rsamtools, rtracklayer, S4Vectors(>= 0.7.20) |
| LinkingTo | |
| Suggests | BiocStyle, biovizBase, devtools (>= 1.6), derfinderData(>= 0.99.0), ggplot2, knitcitations (>= 1.0.1), knitr (>= 1.6), 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | derfinder_1.4.4.tar.gz |
| Windows Binary | derfinder_1.4.4.zip |
| Mac OS X 10.6 (Snow Leopard) | derfinder_1.4.4.tgz |
| Mac OS X 10.9 (Mavericks) | derfinder_1.4.4.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/derfinder/tree/release-3.2 |
| Package Short Url | http://bioconductor.org/packages/derfinder/ |
| Package Downloads Report | Download Stats |
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