DSS: Dispersion shrinakge for sequencing data.
Version 2.16.0

DSS is an R library performing differntial analysis for count-based sequencing data. It detectes differentially expressed genes (DEGs) from RNA-seq, and differentially methylated loci or regions (DML/DMRs) from bisulfite sequencing (BS-seq). The core of DSS is a new dispersion shrinkage method for estimating the dispersion parameter from Gamma-Poisson or Beta-Binomial distributions.

Browse man pages Browse package API and functions Browse package files

AuthorHao Wu <hao.wu@emory.edu>
Bioconductor views ChIPSeq DNAMethylation DifferentialExpression DifferentialMethylation GeneExpression RNASeq Sequencing
Date of publicationNone
MaintainerHao Wu <hao.wu@emory.edu>
LicenseGPL
Version2.16.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("DSS")

Man pages

callDML: Function to detect differntially methylated loci (DML) for...
callDMR: Function to detect differntially methylated regions (DMR) for...
dispersion: Acessor functions for the 'dispersion' slot in a SeqCountData...
DMLfit.multiFactor: Fit a linear model for BS-seq data from general experimental...
DMLtest: Function to perform statistical test of differntially...
DMLtest.multiFactor: Perform statistical test for BS-seq data from general...
DSS.DE: Perform RNA-seq differential expression analysis in two-group...
DSS-package: Dispersion shrinkage for sequencing data
estDispersion: Estimate and shrink tag-specific dipsersions
estNormFactors: Estimate normalization factors
makeBSseqData: Create an object of BSseq class from several data frames.
normalizationFactor: Accessor functions for the 'normalizationFactor' slot in a...
SeqCountSet-class: Class '"SeqCountSet"' - container for count data from...
seqData: A simulated 'SeqCountData' object.
showOneDMR: Visualze the count data for one DMR
waldTest: Perform gene-wise Wald test for two group comparisons for...

Functions

DMLfit.multiFactor Man page Source code
DMLfit.multiFactor.engine Source code
DMLfit.oneCG Source code
DMLtest Man page Source code
DMLtest.Smooth Source code
DMLtest.multiFactor Man page Source code
DMLtest.multiFactor.engine Source code
DMLtest.noSmooth Source code
DSS Man page
DSS-package Man page
DSS.DE Man page Source code
SeqCountSet Man page
SeqCountSet-class Man page
calc.expY Source code
callDML Man page Source code
callDMR Man page Source code
compute.baseSigma.notrend Source code
compute.baseSigma.trend Source code
compute.mean.Smooth Source code
compute.mean.noSmooth Source code
compute.var.Smooth Source code
compute.var.Smooth.old Source code
compute.waldStat.Smooth Source code
compute.waldStat.noSmooth Source code
dbb Source code
dispersion Man page
dispersion,SeqCountSet-method Man page
dispersion.shrinkage.BSseq Source code
dispersion<- Man page
dispersion<-,SeqCountSet,numeric-method Man page
est.dispersion Source code
est.dispersion.BSseq Source code
est.phi.naive Source code
est.phi0 Source code
est.prior.BSseq.logN Source code
est.trend Source code
estDispersion Man page Source code
estDispersion,SeqCountSet-method Man page
estDispersion.multiFactor Source code
estDispersion.notrend Source code
estDispersion.trend Source code
estNormFactors Man page Source code
estNormFactors,SeqCountSet-method Man page
estNormFactors.lr Source code
estNormFactors.median Source code
estNormFactors.quantile Source code
estNormFactors.total Source code
find.factor Source code
findBumps Source code
findRegion Source code
getBSseqIndex Source code
hasCoverage Source code
loccov Source code
loccov2 Source code
locfdr Source code
locmle Source code
lrTest Source code
makeBSseqData Man page Source code
makeDesign Source code
mergeData.counts Source code
mergeData.counts.smooth Source code
newSeqCountSet Man page Source code
normalizationFactor Man page
normalizationFactor,SeqCountSet-method Man page
normalizationFactor<- Man page
normalizationFactor<-,SeqCountSet,matrix-method Man page
normalizationFactor<-,SeqCountSet,numeric-method Man page
rnegbinom Source code
rowVars Source code Source code
scv Source code
seqData Man page
showOneDMR Man page Source code
shrink.dispersion.notrend Source code
shrink.dispersion.trend Source code
smooth.chr Source code
smooth.collapse Source code
sortPos Source code
waldTest Man page Source code
waldTest,SeqCountSet-method Man page
waldTest.DML Source code

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/BSseq_plots.R
R/BSseq_util.R
R/DML.R
R/DML.multiFactor.R
R/DMR.R
R/RNAseqWrapper.R
R/estDispersion.R
R/estDispersion.multiFactor.R
R/estDispersion.notrend.R
R/estDispersion.trend.R
R/estDispersion.util.R
R/locfdr.R
R/locfns.R
R/lrtest.R
R/normalization.R
R/util.R
R/waldTest.R
build
build/vignette.rds
data
data/RRBS.RData
data/seqData.rda
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/DSS.R
inst/doc/DSS.Rnw
inst/doc/DSS.pdf
inst/extdata
inst/extdata/cond1_1.txt
inst/extdata/cond1_2.txt
inst/extdata/cond2_1.txt
inst/extdata/cond2_2.txt
man
man/DMLfit.multiFactor.Rd
man/DMLtest.Rd
man/DMLtest.multiFactor.Rd
man/DSS-package.Rd
man/DSS.DE.Rd
man/SeqCountSet-class.Rd
man/callDML.Rd
man/callDMR.Rd
man/dispersion.Rd
man/estDispersion.Rd
man/estNormFactors.Rd
man/makeBSseqData.Rd
man/normalizationFactor.Rd
man/seqData.Rd
man/showOneDMR.Rd
man/waldTest.Rd
src
src/DSS.h
src/compute_var_smooth.c
src/filter.c
src/nitem.c
vignettes
vignettes/DSS.Rnw
vignettes/aDMR.pdf
DSS documentation built on May 20, 2017, 10:49 p.m.