qsea
IP-seq data analysis and vizualization
Bioconductor version: 3.23 · Package version: 1.38.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("qsea")Details
| Maintainer | Matthias Lienhard <lienhard@molgen.mpg.de> |
| Author | Matthias Lienhard [aut, cre] (ORCID: <https://orcid.org/0000-0002-2549-3142>), Lukas Chavez [aut] (ORCID: <https://orcid.org/0000-0002-8718-8848>), Ralf Herwig [aut] (ORCID: <https://orcid.org/0000-0002-9335-1760>) |
| License | GPL-2 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | ChIPSeq, ChipOnChip, CopyNumberVariation, CpGIsland, DNAMethylation, DifferentialMethylation, Normalization, Preprocessing, QualityControl, Sequencing, Software, Visualization |
| Package Short Url | https://bioconductor.org/packages/qsea/ |
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 1.38.0, https://bioconductor.org/packages/qsea.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | qsea_1.38.0.tar.gz |
| Windows binary (x86_64) | qsea_1.38.0.zip |
| macOS binary (arm64) | qsea_1.38.0.tgz |
| macOS binary (x86_64) | qsea_1.38.0.tgz |
Dependencies
Depends: R (>= 4.3)
Imports: Biostrings, graphics, gtools, methods, stats, utils, HMMcopy, rtracklayer, BSgenome, GenomicRanges, Rsamtools, IRanges, limma, Seqinfo, BiocGenerics, grDevices, zoo, BiocParallel, S4Vectors
Suggests: BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, testthat, BiocStyle, knitr, rmarkdown, BiocManager, MASS
Reverse dependencies
Suggests Me (1): MEDIPSData