qsea
IP-seq data analysis and vizualization
Bioconductor version: Release (3.20)
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")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | 1.32.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (8 years) |
| License | GPL-2 |
| Depends | R (>= 4.3) |
| Imports | Biostrings, graphics, gtools, methods, stats, utils, HMMcopy, rtracklayer, BSgenome, GenomicRanges, Rsamtools, IRanges, limma, GenomeInfoDb, 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 | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | qsea_1.32.0.tar.gz |
| Windows Binary (x86_64) | qsea_1.32.0.zip |
| macOS Binary (x86_64) | qsea_1.32.0.tgz |
| macOS Binary (arm64) | qsea_1.31.0.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 |