To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("qsea")

In most cases, you don't need to download the package archive at all.

qsea

DOI: 10.18129/B9.bioc.qsea    

IP-seq data analysis and vizualization

Bioconductor version: Release (3.6)

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

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

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("qsea")

Documentation

HTML R Script qsea
PDF   Reference Manual
Text   NEWS

Details

biocViews ChIPSeq, ChipOnChip, CopyNumberVariation, CpGIsland, DNAMethylation, DifferentialMethylation, Normalization, Preprocessing, QualityControl, Sequencing, Software, Visualization
Version 1.4.0
In Bioconductor since BioC 3.4 (R-3.3) (1 year)
License GPL (>=2)
Depends R (>= 3.3)
Imports Biostrings, graphics, gtools, methods, stats, utils, HMMcopy, rtracklayer, BSgenome, GenomicRanges, Rsamtools, IRanges, limma, GenomeInfoDb, BiocGenerics, grDevices, zoo, BiocParallel
LinkingTo
Suggests BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, testthat, BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Source Package qsea_1.4.0.tar.gz
Windows Binary qsea_1.4.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) qsea_1.4.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/qsea
Package Short Url http://bioconductor.org/packages/qsea/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: