Package: DSS 2.61.0

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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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
DSS/json (API)

# Install 'DSS' in R:

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

Datasets:

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

On BioConductor:DSS-2.61.0(bioc 3.24)DSS-2.60.0(bioc 3.23)

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

sequencing rnaseq dnamethylation geneexpression differentialexpression differentialmethylation

7.21 score 4 packages 328 scripts 1.4k downloads 288 mentions 16 exports 82 dependencies

Last updated from:8a73abe69f. Checks:1 ERROR, 11 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	213
linux-devel-arm64	WARNING	300
linux-devel-x86_64	WARNING	445
source / vignettes	OK	279
linux-release-arm64	WARNING	300
linux-release-x86_64	WARNING	349
macos-release-arm64	WARNING	308
macos-release-x86_64	WARNING	510
macos-oldrel-arm64	WARNING	238
macos-oldrel-x86_64	WARNING	427
windows-devel-x86_64	WARNING	295
windows-release-x86_64	WARNING	331
windows-oldrel-x86_64	WARNING	333
wasm-release	OK	161

Exports:callDML callDMR dispersion dispersion<-DMLfit.multiFactor DMLtest DMLtest.multiFactor DSS.DE estDispersion estNormFactors makeBSseqData newSeqCountSet normalizationFactor normalizationFactor<-showOneDMR waldTest

Dependencies:abind askpass assorthead beachmat BH Biobase BiocBaseUtils BiocGenerics BiocIO biocmake BiocParallel Biostrings bitops BSgenome bsseq cigarillo cli codetools cpp11 crayon curl data.table DelayedArray DelayedMatrixStats dir.expiry farver filelock formatR futile.logger futile.options generics GenomicAlignments GenomicRanges glue gtools h5mread HDF5Array httr IRanges jsonlite labeling lambda.r lattice lifecycle limma locfit Matrix MatrixGenerics matrixStats mime openssl permute R.methodsS3 R.oo R.utils R6 RColorBrewer Rcpp RCurl restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang Rsamtools rtracklayer S4Arrays S4Vectors scales Seqinfo snow SparseArray sparseMatrixStats statmod SummarizedExperiment sys viridisLite XML XVector yaml

The DSS User's Guide

Rendered fromDSS.Rmdusingknitr::rmarkdown

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

Help page	Topics
Dispersion shrinkage for sequencing data	DSS-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 dataset	design
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 design	DMLfit.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 design	DMLtest.multiFactor
Perform RNA-seq differential expression analysis in two-group comparison	DSS.DE
Estimate and shrink tag-specific dipsersions	estDispersion estDispersion,SeqCountSet-method
Estimate normalization factors	estNormFactors 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 design	RRBS
Class '"SeqCountSet"' - container for count data from sequencing experiment	newSeqCountSet SeqCountSet SeqCountSet-class
A simulated 'SeqCountData' object.	seqData
Visualze the count data for one DMR	showOneDMR
Perform gene-wise Wald test for two group comparisons for sequencing count data.	waldTest waldTest,SeqCountSet-method

Package: DSS 2.61.0

DSS: Dispersion shrinkage for sequencing data

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