- recipe bioconductor-epimutacions
Robust outlier identification for DNA methylation data
- Homepage:
https://bioconductor.org/packages/3.18/bioc/html/epimutacions.html
- License:
MIT + file LICENSE
- Recipe:
The package includes some statistical outlier detection methods for epimutations detection in DNA methylation data. The methods included in the package are MANOVA, Multivariate linear models, isolation forest, robust mahalanobis distance, quantile and beta. The methods compare a case sample with a suspected disease against a reference panel (composed of healthy individuals) to identify epimutations in the given case sample. It also contains functions to annotate and visualize the identified epimutations.
- package bioconductor-epimutacions¶
- versions:
1.6.1-0,1.4.0-0,1.2.0-1,1.2.0-0- depends bioconductor-annotationdbi:
>=1.64.0,<1.65.0- depends bioconductor-annotationdbi:
>=1.64.1,<1.65.0a0- depends bioconductor-annotationhub:
>=3.10.0,<3.11.0- depends bioconductor-annotationhub:
>=3.10.0,<3.11.0a0- depends bioconductor-biocgenerics:
>=0.48.0,<0.49.0- depends bioconductor-biocgenerics:
>=0.48.1,<0.49.0a0- depends bioconductor-biocparallel:
>=1.36.0,<1.37.0- depends bioconductor-biocparallel:
>=1.36.0,<1.37.0a0- depends bioconductor-biomart:
>=2.58.0,<2.59.0- depends bioconductor-biomart:
>=2.58.0,<2.59.0a0- depends bioconductor-bumphunter:
>=1.44.0,<1.45.0- depends bioconductor-bumphunter:
>=1.44.0,<1.45.0a0- depends bioconductor-ensembldb:
>=2.26.0,<2.27.0- depends bioconductor-ensembldb:
>=2.26.0,<2.27.0a0- depends bioconductor-epimutacionsdata:
>=1.6.0,<1.7.0- depends bioconductor-epimutacionsdata:
>=1.6.0,<1.7.0a0- depends bioconductor-experimenthub:
>=2.10.0,<2.11.0- depends bioconductor-experimenthub:
>=2.10.0,<2.11.0a0- depends bioconductor-genomeinfodb:
>=1.38.0,<1.39.0- depends bioconductor-genomeinfodb:
>=1.38.1,<1.39.0a0- depends bioconductor-genomicfeatures:
>=1.54.0,<1.55.0- depends bioconductor-genomicfeatures:
>=1.54.1,<1.55.0a0- depends bioconductor-genomicranges:
>=1.54.0,<1.55.0- depends bioconductor-genomicranges:
>=1.54.1,<1.55.0a0- depends bioconductor-gviz:
>=1.46.0,<1.47.0- depends bioconductor-gviz:
>=1.46.1,<1.47.0a0- depends bioconductor-homo.sapiens:
>=1.3.0,<1.4.0- depends bioconductor-homo.sapiens:
>=1.3.1,<1.4.0a0- depends bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19:
>=0.6.0,<0.7.0- depends bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19:
>=0.6.1,<0.7.0a0- depends bioconductor-illuminahumanmethylation450kmanifest:
>=0.4.0,<0.5.0- depends bioconductor-illuminahumanmethylation450kmanifest:
>=0.4.0,<0.5.0a0- depends bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19:
>=0.6.0,<0.7.0- depends bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19:
>=0.6.0,<0.7.0a0- depends bioconductor-illuminahumanmethylationepicmanifest:
>=0.3.0,<0.4.0- depends bioconductor-illuminahumanmethylationepicmanifest:
>=0.3.0,<0.4.0a0- depends bioconductor-iranges:
>=2.36.0,<2.37.0- depends bioconductor-iranges:
>=2.36.0,<2.37.0a0- depends bioconductor-minfi:
>=1.48.0,<1.49.0- depends bioconductor-minfi:
>=1.48.0,<1.49.0a0- 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-summarizedexperiment:
>=1.32.0,<1.33.0- depends bioconductor-summarizedexperiment:
>=1.32.0,<1.33.0a0- depends bioconductor-txdb.hsapiens.ucsc.hg18.knowngene:
>=3.2.0,<3.3.0- depends bioconductor-txdb.hsapiens.ucsc.hg18.knowngene:
>=3.2.2,<3.3.0a0- depends bioconductor-txdb.hsapiens.ucsc.hg19.knowngene:
>=3.2.0,<3.3.0- depends bioconductor-txdb.hsapiens.ucsc.hg19.knowngene:
>=3.2.2,<3.3.0a0- depends bioconductor-txdb.hsapiens.ucsc.hg38.knowngene:
>=3.18.0,<3.19.0- depends bioconductor-txdb.hsapiens.ucsc.hg38.knowngene:
>=3.18.0,<3.19.0a0- 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-ggplot2:
- depends r-ggrepel:
- depends r-gridextra:
- depends r-isotree:
- depends r-matrixstats:
- depends r-purrr:
- depends r-reshape2:
- depends r-robustbase:
- depends r-tibble:
- 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-epimutacions and update with:: mamba update bioconductor-epimutacions
To create a new environment, run:
mamba create --name myenvname bioconductor-epimutacions
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-epimutacions:<tag> (see `bioconductor-epimutacions/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
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