Package: DSS 2.55.0

Hao Wu

DSS: Dispersion shrinkage 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.

Authors:Hao Wu<[email protected]>, Hao Feng<[email protected]>

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DSS.pdf |DSS.html✨
DSS/json (API)
NEWS

# Install 'DSS' in R:
install.packages('DSS', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • RRBS - An example dataset for multiple factor design
  • design - Experimental design for the example RRBS dataset
  • seqData - A simulated 'SeqCountData' object.

On BioConductor:DSS-2.55.0(bioc 3.21)DSS-2.54.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

sequencingrnaseqdnamethylationgeneexpressiondifferentialexpressiondifferentialmethylation

7.30 score 5 packages 233 scripts 1.4k downloads 288 mentions 16 exports 81 dependencies

Last updated 2 months agofrom:23fba501be. Checks:OK: 1 WARNING: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 25 2024
R-4.5-win-x86_64WARNINGNov 25 2024
R-4.5-linux-x86_64WARNINGNov 25 2024
R-4.4-win-x86_64WARNINGNov 25 2024
R-4.4-mac-x86_64WARNINGNov 25 2024
R-4.4-mac-aarch64WARNINGNov 25 2024
R-4.3-win-x86_64WARNINGNov 25 2024
R-4.3-mac-x86_64WARNINGNov 25 2024
R-4.3-mac-aarch64WARNINGNov 25 2024

Exports:callDMLcallDMRdispersiondispersion<-DMLfit.multiFactorDMLtestDMLtest.multiFactorDSS.DEestDispersionestNormFactorsmakeBSseqDatanewSeqCountSetnormalizationFactornormalizationFactor<-showOneDMRwaldTest

Dependencies:abindaskpassassortheadbeachmatBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsBSgenomebsseqclicodetoolscolorspacecpp11crayoncurldata.tableDelayedArrayDelayedMatrixStatsfarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesgluegtoolsHDF5ArrayhttrIRangesjsonlitelabelinglambda.rlatticelifecyclelimmalocfitMatrixMatrixGenericsmatrixStatsmimemunsellopensslpermuteR.methodsS3R.ooR.utilsR6RColorBrewerRcppRCurlrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsscalessnowSparseArraysparseMatrixStatsstatmodSummarizedExperimentsysUCSC.utilsviridisLiteXMLXVectoryamlzlibbioc

The DSS User's Guide

Hao Wu, [email protected]

Rendered fromDSS.Rmdusingknitr::rmarkdownon Nov 25 2024.

Last update: 2022-08-02
Started: 2019-04-26

Readme and manuals

Help Manual

Help pageTopics
Dispersion shrinkage for sequencing dataDSS-package DSS
Function to detect differntially methylated loci (DML) from bisulfite sequencing (BS-seq) data.callDML
Function to detect differntially methylated regions (DMR) from bisulfite sequencing (BS-seq) data.callDMR
Experimental design for the example RRBS datasetdesign
Acessor functions for the 'dispersion' slot in a SeqCountData object.dispersion dispersion,SeqCountSet-method dispersion<- dispersion<-,SeqCountSet,numeric-method
Fit a linear model for BS-seq data from general experimental designDMLfit.multiFactor
Function to perform statistical test of differntially methylated loci (DML) for two group comparisons of bisulfite sequencing (BS-seq) data.DMLtest
Perform statistical test for BS-seq data from general experimental designDMLtest.multiFactor
Perform RNA-seq differential expression analysis in two-group comparisonDSS.DE
Estimate and shrink tag-specific dipsersionsestDispersion estDispersion,SeqCountSet-method
Estimate normalization factorsestNormFactors estNormFactors,SeqCountSet-method
Create an object of BSseq class from several data frames.makeBSseqData
Accessor functions for the 'normalizationFactor' slot in a SeqCountData object.normalizationFactor normalizationFactor,SeqCountSet-method normalizationFactor<- normalizationFactor<-,SeqCountSet,matrix-method normalizationFactor<-,SeqCountSet,numeric-method
An example dataset for multiple factor designRRBS
Class '"SeqCountSet"' - container for count data from sequencing experimentnewSeqCountSet SeqCountSet SeqCountSet-class
A simulated 'SeqCountData' object.seqData
Visualze the count data for one DMRshowOneDMR
Perform gene-wise Wald test for two group comparisons for sequencing count data.waldTest waldTest,SeqCountSet-method