BiSeq
This is the development version of BiSeq; for the stable release version, see BiSeq.
Processing and analyzing bisulfite sequencing data
Bioconductor version: Development (3.24)
The BiSeq package provides useful classes and functions to handle and analyze targeted bisulfite sequencing (BS) data such as reduced-representation bisulfite sequencing (RRBS) data. In particular, it implements an algorithm to detect differentially methylated regions (DMRs). The package takes already aligned BS data from one or multiple samples.
Author: Katja Hebestreit, Hans-Ulrich Klein
Maintainer: Katja Hebestreit <katja.hebestreit at gmail.com>
citation("BiSeq")):
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("BiSeq")
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("BiSeq")| An Introduction to BiSeq | R Script | |
| Reference Manual |
Details
| biocViews | DNAMethylation, Genetics, MethylSeq, Sequencing, Software |
| Version | 1.53.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) (13.5 years) |
| License | LGPL-3 |
| Depends | R (>= 3.5.0), methods, S4Vectors, IRanges(>= 1.17.24), GenomicRanges, SummarizedExperiment(>= 0.2.0), Formula |
| Imports | methods, BiocGenerics, Biobase, S4Vectors, IRanges, Seqinfo, GenomicRanges, SummarizedExperiment, rtracklayer, parallel, betareg, lokern, Formula, globaltest |
| System Requirements | |
| URL |
See More
| Suggests | |
| Linking To | |
| Enhances | |
| Depends On Me | RRBSdata |
| Imports Me | |
| Suggests Me | updateObject |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | BiSeq_1.53.0.tar.gz |
| Windows Binary (x86_64) | BiSeq_1.53.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | BiSeq_1.53.0.tgz |
| macOS Binary (sonoma-arm64) | BiSeq_1.53.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/BiSeq |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/BiSeq |
| Bioc Package Browser | https://code.bioconductor.org/browse/BiSeq/ |
| Package Short Url | https://bioconductor.org/packages/BiSeq/ |
| Package Downloads Report | Download Stats |