- recipe bioconductor-methylkit
DNA methylation analysis from high-throughput bisulfite sequencing results
- Homepage:
https://bioconductor.org/packages/3.18/bioc/html/methylKit.html
- License:
Artistic-2.0
- Recipe:
- Links:
biotools: methylkit
methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods and whole genome bisulfite sequencing. It also has functions to analyze base-pair resolution 5hmC data from experimental protocols such as oxBS-Seq and TAB-Seq. Methylation calling can be performed directly from Bismark aligned BAM files.
- package bioconductor-methylkit¶
- versions:
1.28.0-1,1.28.0-0,1.26.0-0,1.24.0-1,1.24.0-0,1.20.0-2,1.20.0-1,1.20.0-0,1.18.0-0,1.28.0-1,1.28.0-0,1.26.0-0,1.24.0-1,1.24.0-0,1.20.0-2,1.20.0-1,1.20.0-0,1.18.0-0,1.16.1-0,1.16.0-0,1.14.1-0,1.12.0-0,1.10.0-1,1.8.1-0,1.8.0-0,1.6.3-0,1.4.0-0,1.2.4-0,1.0.0-0,0.99.2-0- depends bioconductor-fastseg:
>=1.48.0,<1.49.0- depends bioconductor-fastseg:
>=1.48.0,<1.49.0a0- depends bioconductor-genomeinfodb:
>=1.38.0,<1.39.0- depends bioconductor-genomeinfodb:
>=1.38.1,<1.39.0a0- depends bioconductor-genomicranges:
>=1.54.0,<1.55.0- depends bioconductor-genomicranges:
>=1.54.1,<1.55.0a0- depends bioconductor-iranges:
>=2.36.0,<2.37.0- depends bioconductor-iranges:
>=2.36.0,<2.37.0a0- depends bioconductor-limma:
>=3.58.0,<3.59.0- depends bioconductor-limma:
>=3.58.1,<3.59.0a0- depends bioconductor-qvalue:
>=2.34.0,<2.35.0- depends bioconductor-qvalue:
>=2.34.0,<2.35.0a0- depends bioconductor-rhtslib:
>=2.4.0,<2.5.0- depends bioconductor-rhtslib:
>=2.4.0,<2.5.0a0- depends bioconductor-rsamtools:
>=2.18.0,<2.19.0- depends bioconductor-rsamtools:
>=2.18.0,<2.19.0a0- depends bioconductor-rtracklayer:
>=1.62.0,<1.63.0- depends bioconductor-rtracklayer:
>=1.62.0,<1.63.0a0- depends bioconductor-s4vectors:
>=0.40.0,<0.41.0- depends bioconductor-s4vectors:
>=0.40.2,<0.41.0a0- depends bioconductor-zlibbioc:
>=1.48.0,<1.49.0- depends bioconductor-zlibbioc:
>=1.48.0,<1.49.0a0- depends libblas:
>=3.9.0,<4.0a0- depends libgcc-ng:
>=12- depends liblapack:
>=3.9.0,<4.0a0- depends libstdcxx-ng:
>=12- depends r-base:
>=4.3,<4.4.0a0- depends r-data.table:
>=1.9.6- depends r-emdbook:
- depends r-gtools:
- depends r-kernsmooth:
- depends r-mclust:
- depends r-mgcv:
- depends r-r.utils:
- depends r-rcpp:
- requirements:
Installation
You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install bioconductor-methylkit and update with:: mamba update bioconductor-methylkit
To create a new environment, run:
mamba create --name myenvname bioconductor-methylkit
with
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).Alternatively, use the docker container:
docker pull quay.io/biocontainers/bioconductor-methylkit:<tag> (see `bioconductor-methylkit/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-methylkit/README.html)
