bsseq
This is thereleased version of bsseq; for the devel version, seebsseq.
Analyze, manage and store whole-genome methylation data
Bioconductor version: Release (3.22)
A collection of tools for analyzing and visualizing whole-genome methylation data from sequencing. This includes whole-genome bisulfite sequencing and Oxford nanopore data.
Author: Kasper Daniel Hansen [aut, cre]
ORCID: 0000-0003-0086-0687, Peter Hickey [aut] ORCID: 0000-0002-8153-6258, Hervé Pagès [ctb], Aaron Lun [ctb]
Maintainer: Kasper Daniel Hansen <kasperdanielhansen at gmail.com>
citation("bsseq")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("bsseq")For older versions of R, please refer to the appropriateBioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("bsseq")| Analyzing WGBS data with bsseq | HTML | R Script |
| bsseq User's Guide | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DNAMethylation,Software |
| Version | 1.46.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) (13 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.0), methods,BiocGenerics,GenomicRanges(>= 1.41.5),SummarizedExperiment(>= 1.19.5) |
| Imports | IRanges(>= 2.23.9),Seqinfo,scales, stats, parallel, tools, graphics,Biobase,locfit,gtools,data.table (>= 1.11.8),S4Vectors(>= 0.27.12),R.utils (>= 2.0.0),DelayedMatrixStats(>= 1.5.2),permute,limma,DelayedArray(>= 0.15.16),Rcpp,BiocParallel,BSgenome,Biostrings, utils,HDF5Array(>= 1.19.11),rhdf5,beachmat(>= 2.23.2) |
| System Requirements | C++17 |
| URL | https://github.com/kasperdanielhansen/bsseq |
| Bug Reports | https://github.com/kasperdanielhansen/bsseq/issues |
See More
| Suggests | testthat,bsseqData,BiocStyle,rmarkdown,knitr,Matrix,doParallel,rtracklayer,BSgenome.Hsapiens.UCSC.hg38,batchtools |
| Linking To | Rcpp,beachmat,assorthead(>= 1.1.4) |
| Enhances | |
| Depends On Me | biscuiteer,dmrseq,DSS,bsseqData |
| Imports Me | borealis,DMRcate,methylCC,methylSig,MIRA,NanoMethViz,scmeth,SOMNiBUS |
| Suggests Me | iscream,methrix,tissueTreg |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | bsseq_1.46.0.tar.gz |
| Windows Binary (x86_64) | bsseq_1.46.0.zip |
| macOS Binary (x86_64) | bsseq_1.46.0.tgz |
| macOS Binary (arm64) | bsseq_1.46.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/bsseq |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/bsseq |
| Bioc Package Browser | https://code.bioconductor.org/browse/bsseq/ |
| Package Short Url | https://bioconductor.org/packages/bsseq/ |
| Package Downloads Report | Download Stats |