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>

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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) (1.5 years)
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
Suggests BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, testthat, BiocStyle, knitr, rmarkdown
Depends On Me
Imports Me
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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/
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