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This is the development version of qsea; for the stable release version, see qsea.

IP-seq data analysis and vizualization

Bioconductor version: Development (3.20)

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 [aut, cre] , Lukas Chavez [aut] , Ralf Herwig [aut]

Maintainer: Matthias Lienhard <lienhard at>

Citation (from within R, enter citation("qsea")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

qsea HTML R Script
Reference Manual PDF


biocViews ChIPSeq, ChipOnChip, CopyNumberVariation, CpGIsland, DNAMethylation, DifferentialMethylation, Normalization, Preprocessing, QualityControl, Sequencing, Software, Visualization
Version 1.31.0
In Bioconductor since BioC 3.4 (R-3.3) (7.5 years)
License GPL-2
Depends R (>= 4.3)
Imports Biostrings, graphics, gtools, methods, stats, utils, HMMcopy, rtracklayer, BSgenome, GenomicRanges, Rsamtools, IRanges, limma, GenomeInfoDb, BiocGenerics, grDevices, zoo, BiocParallel, S4Vectors
System Requirements
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Suggests BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, testthat, BiocStyle, knitr, rmarkdown, BiocManager, MASS
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Follow Installation instructions to use this package in your R session.

Source Package qsea_1.31.0.tar.gz
Windows Binary
macOS Binary (x86_64) qsea_1.31.0.tgz
macOS Binary (arm64) qsea_1.31.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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