bsseq
Analyze, manage and store whole-genome methylation data
Bioconductor version: 3.24 · Package version: 1.49.2
A collection of tools for analyzing and visualizing whole-genome methylation data from sequencing. This includes whole-genome bisulfite sequencing and Oxford nanopore data.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("bsseq")Details
| Maintainer | Kasper Daniel Hansen <kasperdanielhansen@gmail.com> |
| Author | Kasper Daniel Hansen [aut, cre] (ORCID: <https://orcid.org/0000-0003-0086-0687>), Peter Hickey [aut] (ORCID: <https://orcid.org/0000-0002-8153-6258>), Hervé Pagès [ctb], Aaron Lun [ctb] |
| License | Artistic-2.0 |
| URL | https://github.com/kasperdanielhansen/bsseq |
| Bug Reports | https://github.com/kasperdanielhansen/bsseq/issues |
| System Requirements | C++17 |
| Downloads rank | 2238 |
| Source branch | devel |
| biocViews | DNAMethylation, Software |
Documentation
- Analyzing WGBS data with bsseq
- The bsseq User's Guide
- Importing and filtering long-read modification data with bsseq
Download
Follow the installation instructions to use this package in your R session.
| Source package | bsseq_1.49.2.tar.gz |
| Windows binary (x86_64) | bsseq_1.49.2.zip |
| macOS binary (arm64) | bsseq_1.49.2.tgz |
| macOS binary (x86_64) | bsseq_1.49.2.tgz |
Dependencies
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)
LinkingTo: Rcpp, beachmat, assorthead (>= 1.1.4)
Suggests: testthat, bsseqData, BiocStyle, rmarkdown, knitr, Matrix, doParallel, rtracklayer, BSgenome.Hsapiens.UCSC.hg38, batchtools, tidyverse
Reverse dependencies
Depends On Me (4): biscuiteer, bsseqData, dmrseq, DSS
Imports Me (11): borealis, DMRcate, epiSeeker, methodical, methylCC, methylSig, MIRA, NanoMethViz, RBedMethyl, scmeth, SOMNiBUS
Suggests Me (4): iscream, methFuse, methrix, tissueTreg