qsea

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

IP-seq data analysis and vizualization

Bioconductor version: Development (3.21)

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: ), Lukas Chavez [aut] (ORCID: ), Ralf Herwig [aut] (ORCID: )

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

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

Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
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	1.33.0
In Bioconductor since	BioC 3.4 (R-3.3) (8 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

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

Package Archives

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

Source Package	qsea_1.33.0.tar.gz
Windows Binary (x86_64)	qsea_1.33.0.zip (64-bit only)
macOS Binary (x86_64)
macOS Binary (arm64)
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