qsea: IP-seq data analysis and vizualization

qsea (quantitative sequencing enrichment analysis) was developed as the successor of the MEDIPS package for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq). However, qsea provides several functionalities for the analysis of other kinds of quantitative sequencing data (e.g. ChIP-seq, MBD-seq, CMS-seq and others) including calculation of differential enrichment between groups of samples.

Install the latest version of this package by entering the following in R:
AuthorMatthias Lienhard, Lukas Chavez, Ralf Herwig
Bioconductor views ChIPSeq ChipOnChip CopyNumberVariation CpGIsland DNAMethylation DifferentialMethylation Normalization Preprocessing QualityControl Sequencing Visualization
Date of publicationNone
MaintainerMatthias Lienhard <lienhard@molgen.mpg.de>
LicenseGPL (>=2)

View on Bioconductor


addCNV Man page
addContrast Man page
addCoverage Man page
addEnrichmentParameters Man page
addLibraryFactors Man page
addNewSamples Man page
addOffset Man page
addParameters,qseaGLM-method Man page
addParameters,qseaSet-method Man page
addPatternDensity Man page
addSeqPref Man page
createQseaSet Man page
fitNBglm Man page
getChrNames Man page
getChrNames,qseaSet-method Man page
getCNV Man page
getCNV,qseaSet-method Man page
getCounts Man page
getCounts,qseaSet-method Man page
getExampleQseaSet Man page
getLibSize Man page
getLibSize,qseaSet-method Man page
getNormFactors Man page
getNormFactors,qseaSet-method Man page
getOffset Man page
getOffset,qseaSet-method Man page
getParameters Man page
getParameters,qseaGLM-method Man page
getParameters,qseaSet-method Man page
getPCA Man page
getRegions Man page
getRegions,qseaSet-method Man page
getSampleGroups Man page
getSampleGroups,qseaSet-method Man page
getSampleNames Man page
getSampleNames,qseaGLM-method Man page
getSampleNames,qseaPCA-method Man page
getSampleNames,qseaSet-method Man page
getSampleTable Man page
getSampleTable,qseaSet-method Man page
getWindowSize Man page
getWindowSize,qseaSet-method Man page
getZygosity Man page
getZygosity,qseaSet-method Man page
hasCNV Man page
hasCNV,qseaSet-method Man page
isSignificant Man page
makeTable Man page
normMethod Man page
plotCNV Man page
plotCoverage Man page
plotEnrichmentProfile Man page
plotEPmatrix Man page
plotPCA Man page
plotPCAfactors Man page
plotPCAfactors,qseaPCA-method Man page
plotPCA,qseaPCA-method Man page
qsea Man page
QSEA Man page
qseaGLM Man page
qseaGLM-class Man page
qsea-package Man page
qseaPCA Man page
qseaPCA-class Man page
qseaSet Man page
qseaSet-class Man page
regionStats Man page
setZygosity Man page
setZygosity,qseaSet-method Man page
show,qseaGLM-method Man page
show,qseaPCA-method Man page
show,qseaSet-method Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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