DSS: Dispersion shrinakge for sequencing data.

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.

Author
Hao Wu <hao.wu@emory.edu>
Date of publication
None
Maintainer
Hao Wu <hao.wu@emory.edu>
License
GPL
Version
2.14.0

View on Bioconductor

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...

Files in this package

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