qsea
This is the development version of qsea; for the stable release version, see qsea.
IP-seq data analysis and vizualization
Bioconductor version: Development (3.24)
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]
, Lukas Chavez [aut]
, Ralf Herwig [aut]
Maintainer: Matthias Lienhard <lienhard at molgen.mpg.de>
citation("qsea")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text |
Details
| biocViews | ChIPSeq, ChipOnChip, CopyNumberVariation, CpGIsland, DNAMethylation, DifferentialMethylation, Normalization, Preprocessing, QualityControl, Sequencing, Software, Visualization |
| Version | 1.39.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (10 years) |
| License | GPL-2 |
| Depends | R (>= 4.3) |
| Imports | Biostrings, graphics, gtools, methods, stats, utils, HMMcopy, rtracklayer, BSgenome, GenomicRanges, Rsamtools, IRanges, limma, Seqinfo, BiocGenerics, grDevices, zoo, BiocParallel, S4Vectors |
| System Requirements | |
| URL |
See More
| Suggests | BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, testthat, BiocStyle, knitr, rmarkdown, BiocManager, MASS |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | MEDIPSData |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | qsea_1.39.0.tar.gz |
| Windows Binary (x86_64) | qsea_1.39.0.zip |
| macOS Binary (big-sur-x86_64) | qsea_1.39.0.tgz |
| macOS Binary (sonoma-arm64) | qsea_1.39.0.tgz |
| 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 |