- recipe bioconductor-missmethyl
Analysing Illumina HumanMethylation BeadChip Data
- Homepage:
https://bioconductor.org/packages/3.16/bioc/html/missMethyl.html
- License:
GPL-2
- Recipe:
- Links:
biotools: missmethyl
Normalisation, testing for differential variability and differential methylation and gene set testing for data from Illumina's Infinium HumanMethylation arrays. The normalisation procedure is subset-quantile within-array normalisation (SWAN), which allows Infinium I and II type probes on a single array to be normalised together. The test for differential variability is based on an empirical Bayes version of Levene's test. Differential methylation testing is performed using RUV, which can adjust for systematic errors of unknown origin in high-dimensional data by using negative control probes. Gene ontology analysis is performed by taking into account the number of probes per gene on the array, as well as taking into account multi-gene associated probes.
- package bioconductor-missmethyl¶
-
- Versions:
1.32.0-0
,1.26.0-0
,1.24.0-1
,1.24.0-0
,1.22.0-0
,1.20.0-0
,1.18.0-1
,1.16.0-0
,1.14.0-0
,1.32.0-0
,1.26.0-0
,1.24.0-1
,1.24.0-0
,1.22.0-0
,1.20.0-0
,1.18.0-1
,1.16.0-0
,1.14.0-0
,1.12.0-0
- Depends:
bioconductor-annotationdbi
>=1.60.0,<1.61.0
bioconductor-biobase
>=2.58.0,<2.59.0
bioconductor-biocgenerics
>=0.44.0,<0.45.0
bioconductor-genomicranges
>=1.50.0,<1.51.0
bioconductor-go.db
>=3.16.0,<3.17.0
bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19
>=0.6.0,<0.7.0
bioconductor-illuminahumanmethylation450kmanifest
>=0.4.0,<0.5.0
bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19
>=0.6.0,<0.7.0
bioconductor-illuminahumanmethylationepicmanifest
>=0.3.0,<0.4.0
bioconductor-iranges
>=2.32.0,<2.33.0
bioconductor-limma
>=3.54.0,<3.55.0
bioconductor-methylumi
>=2.44.0,<2.45.0
bioconductor-minfi
>=1.44.0,<1.45.0
bioconductor-org.hs.eg.db
>=3.16.0,<3.17.0
bioconductor-s4vectors
>=0.36.0,<0.37.0
bioconductor-summarizedexperiment
>=1.28.0,<1.29.0
r-base
>=4.2,<4.3.0a0
- Required By:
Installation
With an activated Bioconda channel (see set-up-channels), install with:
conda install bioconductor-missmethyl
and update with:
conda update bioconductor-missmethyl
or use the docker container:
docker pull quay.io/biocontainers/bioconductor-missmethyl:<tag>
(see bioconductor-missmethyl/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-missmethyl/README.html)