qsea

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4

IP-seq data analysis and vizualization

Bioconductor version: Development (3.24)

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] ORCID: 0000-0002-2549-3142 , Lukas Chavez [aut] ORCID: 0000-0002-8718-8848 , Ralf Herwig [aut] ORCID: 0000-0002-9335-1760

Maintainer: Matthias Lienhard <lienhard at molgen.mpg.de>

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

Matthias Lienhard, Lukas Chavez, Ralf Herwig. qsea: IP-seq data analysis and vizualization. doi:10.18129/B9.bioc.qsea, R package version 1.39.0, https://bioconductor.org/packages/qsea.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ChIPSeq, ChipOnChip, CopyNumberVariation, CpGIsland, DNAMethylation, DifferentialMethylation, Normalization, Preprocessing, QualityControl, Sequencing, Software, Visualization
Version	1.39.0
In Bioconductor since	BioC 3.4 (R-3.3) (10 years)
License	GPL-2
Depends	R (>= 4.3)
Imports	Biostrings, graphics, gtools, methods, stats, utils, HMMcopy, rtracklayer, BSgenome, GenomicRanges, Rsamtools, IRanges, limma, Seqinfo, BiocGenerics, grDevices, zoo, BiocParallel, S4Vectors
System Requirements
URL

Suggests	BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, testthat, BiocStyle, knitr, rmarkdown, BiocManager, MASS
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me	MEDIPSData
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	qsea_1.39.0.tar.gz
Windows Binary (x86_64)	qsea_1.39.0.zip
macOS Binary (big-sur-x86_64)	qsea_1.39.0.tgz
macOS Binary (sonoma-arm64)	qsea_1.39.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/qsea
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/qsea
Package Short Url	https://bioconductor.org/packages/qsea/
Package Downloads Report	Download Stats