- recipe bioconductor-methylkit
DNA methylation analysis from high-throughput bisulfite sequencing results
- Homepage
https://bioconductor.org/packages/3.14/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
1.20.0-1
,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
,1.20.0-1
,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
>=1.40.0,<1.41.0
bioconductor-genomeinfodb
>=1.30.0,<1.31.0
bioconductor-genomicranges
>=1.46.0,<1.47.0
bioconductor-iranges
>=2.28.0,<2.29.0
bioconductor-limma
>=3.50.0,<3.51.0
bioconductor-qvalue
>=2.26.0,<2.27.0
bioconductor-rhtslib
>=1.26.0,<1.27.0
bioconductor-rsamtools
>=2.10.0,<2.11.0
bioconductor-rtracklayer
>=1.54.0,<1.55.0
bioconductor-s4vectors
>=0.32.0,<0.33.0
bioconductor-zlibbioc
>=1.40.0,<1.41.0
libblas
>=3.8.0,<4.0a0
libgcc-ng
>=10.3.0
liblapack
>=3.8.0,<4.0a0
libstdcxx-ng
>=10.3.0
r-base
>=4.1,<4.2.0a0
r-data.table
>=1.9.6
- Required By
Installation
With an activated Bioconda channel (see 2. Set up channels), install with:
conda install bioconductor-methylkit
and update with:
conda update bioconductor-methylkit
or 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)