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
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IP-seq data analysis and vizualization
Bioconductor version: Release (3.5)
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 |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | ChIPSeq, ChipOnChip, CopyNumberVariation, CpGIsland, DNAMethylation, DifferentialMethylation, Normalization, Preprocessing, QualityControl, Sequencing, Software, Visualization |
| Version | 1.2.0 |
| 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_1.2.0.tar.gz |
| Windows Binary | qsea_1.2.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | qsea_1.2.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/qsea |
| Package Short Url | http://bioconductor.org/packages/qsea/ |
| Package Downloads Report | Download Stats |
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