To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("bsseq")
In most cases, you don't need to download the package archive at all.
bsseq
Analyze, manage and store bisulfite sequencing data
Bioconductor version: 3.0
Tools for analyzing and visualizing bisulfite sequencing data
Author: Kasper Daniel Hansen [aut, cre]
Maintainer: Kasper Daniel Hansen <kasperdanielhansen at gmail.com>
Citation (from within R,
enter citation("bsseq")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("bsseq")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("bsseq")
| R Script | Analyzing WGBS with bsseq | |
| R Script | The bsseq user's guide | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DNAMethylation, Software |
| Version | 1.2.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) |
| License | Artistic-2.0 |
| Depends | R (>= 2.15), methods, BiocGenerics, IRanges, GenomicRanges, parallel, matrixStats |
| Imports | scales, stats, graphics, Biobase, locfit |
| LinkingTo | |
| Suggests | RUnit, bsseqData |
| SystemRequirements | |
| Enhances | |
| URL | https://github.com/kasperdanielhansen/bsseq |
| Depends On Me | bsseqData |
| Imports Me | DSS |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | bsseq_1.2.0.tar.gz |
| Windows Binary | bsseq_1.2.0.zip |
| Mac OS X 10.6 (Snow Leopard) | bsseq_1.2.0.tgz |
| Mac OS X 10.9 (Mavericks) | bsseq_1.2.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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