recipe bioconductor-doppelgangr

Identify likely duplicate samples from genomic or meta-data

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/doppelgangR.html

License:

GPL (>=2.0)

Recipe:

/bioconductor-doppelgangr/meta.yaml

Links:

biotools: doppelgangr, doi: 10.1093/jnci/djw146

The main function is doppelgangR(), which takes as minimal input a list of ExpressionSet object, and searches all list pairs for duplicated samples. The search is based on the genomic data (exprs(eset)), phenotype/clinical data (pData(eset)), and "smoking guns" - supposedly unique identifiers found in pData(eset).

package bioconductor-doppelgangr

Versions:

1.26.0-0,  1.22.0-0,  1.20.0-0,  1.18.0-1,  1.18.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.10.1-0, 

1.26.0-0,  1.22.0-0,  1.20.0-0,  1.18.0-1,  1.18.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.10.1-0,  1.10.0-0,  1.8.0-0,  1.6.0-0,  1.4.1-0

Depends:

• bioconductor-biobase >=2.58.0,<2.59.0

• bioconductor-biocparallel >=1.32.0,<1.33.0

• bioconductor-impute >=1.72.0,<1.73.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• bioconductor-sva >=3.46.0,<3.47.0

• r-base >=4.2,<4.3.0a0

• r-digest

• r-mnormt

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-doppelgangr

and update with:

conda update bioconductor-doppelgangr

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-doppelgangr:<tag>

(see bioconductor-doppelgangr/tags for valid values for <tag>)

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