derfinder : Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach

Package: derfinder
Type: Package
Title: Annotation-agnostic differential expression analysis of RNA-seq
data at base-pair resolution via the DER Finder approach
Version: 1.6.4
Date: 2016-05-12
Authors@R: c(person("Leonardo", "Collado-Torres", role = c("aut", "cre"), email
= "lcollado@jhu.edu"), person(c("Alyssa", "C."), "Frazee", role = c("aut"),
email = "alyssa.frazee@gmail.com"), person(c("Andrew", "E."), "Jaffe",
role = "aut", email = "andrew.jaffe@libd.org"), person(c("Jeffrey", "T."),
"Leek", role = c("aut", "ths"), email = "jtleek@gmail.com"))
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)
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
VignetteBuilder: knitr
Description: 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.
License: Artistic-2.0
LazyData: true
URL: https://github.com/lcolladotor/derfinder
BugReports: https://github.com/lcolladotor/derfinder/issues
biocViews: DifferentialExpression, Sequencing, RNASeq, ChIPSeq,
DifferentialPeakCalling, Software
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-16 04:56:31 UTC; biocbuild
Author: Leonardo Collado-Torres [aut, cre],
Alyssa C. Frazee [aut],
Andrew E. Jaffe [aut],
Jeffrey T. Leek [aut, ths]
Maintainer: Leonardo Collado-Torres <lcollado@jhu.edu>