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.

Author
Matthias Lienhard, Lukas Chavez, Ralf Herwig
Date of publication
None
Maintainer
Matthias Lienhard <lienhard@molgen.mpg.de>
License
GPL (>=2)
Version
1.0.2

View on Bioconductor

Man pages

addCNV
estimate CNV information and add to qseaSet object
addContrast
fit GLMs to reduced model and test for significance
addCoverage
Import sequencing data
addEnrichmentParameters
Enrichment analysis
addLibraryFactors
Estimate effective library size
addOffset
Estimate background reads
addPatternDensity
Infer sequence pattern density values and add to qseaSet...
addSeqPref
Add sequence preference to qseaSet object
createQseaSet
Prepares a qseaSet Object
example
Simulation of MeDIP seq QSEA set
fitNBglm
Fit GLM for each window
getPCA
Principle Component Analysis (PCA) in QSea
isSignificant
Finds Significant Regions
makeTable
Create a Results Table
normMethod
Definition of normalization procedure
plotCNV
Plots a Heatmap-like Overview of the CNVs
plotCoverage
Plots a genome-browser-like image of a region
plotEnrichmentProfile
Plotting functions for enrichment profiles
plotPCA
Plots for Principle Component Analysis (PCA) in QSEA
qseaGLM-class
qseaGLM class and its methods
qsea-package
QSEA: Quantitative sequencing enrichment analysis and...
qseaPCA-class
qseaPCA class and its methods
qseaSet-class
qseaSet class and its methods
regionStats
Counts the Windows in Regions of Interest

Files in this package

qsea/DESCRIPTION
qsea/NAMESPACE
qsea/NEWS
qsea/R
qsea/R/qsea-classes.R
qsea/R/qsea.addCNV.R
qsea/R/qsea.createSet.R
qsea/R/qsea.example.R
qsea/R/qsea.genomeWindows.R
qsea/R/qsea.getCoverage.R
qsea/R/qsea.glm.R
qsea/R/qsea.makeTable.R
qsea/R/qsea.normalize.R
qsea/R/qsea.plots.R
qsea/R/sysdata.rda
qsea/build
qsea/build/vignette.rds
qsea/inst
qsea/inst/doc
qsea/inst/doc/qsea_tutorial.R
qsea/inst/doc/qsea_tutorial.Rmd
qsea/inst/doc/qsea_tutorial.html
qsea/man
qsea/man/addCNV.Rd
qsea/man/addContrast.Rd
qsea/man/addCoverage.Rd
qsea/man/addEnrichmentParameters.Rd
qsea/man/addLibraryFactors.Rd
qsea/man/addOffset.Rd
qsea/man/addPatternDensity.Rd
qsea/man/addSeqPref.Rd
qsea/man/createQseaSet.Rd
qsea/man/example.Rd
qsea/man/fitNBglm.Rd
qsea/man/getPCA.Rd
qsea/man/isSignificant.Rd
qsea/man/makeTable.Rd
qsea/man/normMethod.Rd
qsea/man/plotCNV.Rd
qsea/man/plotCoverage.Rd
qsea/man/plotEnrichmentProfile.Rd
qsea/man/plotPCA.Rd
qsea/man/qsea-package.Rd
qsea/man/qseaGLM-class.Rd
qsea/man/qseaPCA-class.Rd
qsea/man/qseaSet-class.Rd
qsea/man/regionStats.Rd
qsea/src
qsea/src/lm.c
qsea/tests
qsea/tests/testthat
qsea/tests/testthat.R
qsea/tests/testthat/test_example.R
qsea/tests/testthat/test_glm.R
qsea/vignettes
qsea/vignettes/qseaTutorial.bib
qsea/vignettes/qsea_tutorial.Rmd