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Bioconductor - bsseq (development version)

bsseq

This is the development version of bsseq; for the stable release version, see bsseq.

Analyze, manage and store whole-genome methylation data

Bioconductor version: Development (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 (from within R, enter citation("bsseq")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("bsseq")

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("bsseq")
Details biocViews DNAMethylation, Software Version 1.45.2 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 methrix, tissueTreg Links To Me Build Report Build Report Package Archives

Follow Installation instructions to use this package in your R session.

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