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qsea

IP-seq data analysis and vizualization


Bioconductor version: Release (3.18)

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 molgen.mpg.de>

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("qsea")

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

Documentation

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

browseVignettes("qsea")
qsea HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ChIPSeq, ChipOnChip, CopyNumberVariation, CpGIsland, DNAMethylation, DifferentialMethylation, Normalization, Preprocessing, QualityControl, Sequencing, Software, Visualization
Version 1.28.0
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
URL
See More
Suggests BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, testthat, BiocStyle, knitr, rmarkdown, BiocManager, MASS
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
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Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package qsea_1.28.0.tar.gz
Windows Binary qsea_1.28.0.zip
macOS Binary (x86_64) qsea_1.28.0.tgz
macOS Binary (arm64) qsea_1.28.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/qsea
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/qsea
Bioc Package Browser https://code.bioconductor.org/browse/qsea/
Package Short Url https://bioconductor.org/packages/qsea/
Package Downloads Report Download Stats