recipe bioconductor-biscuiteer

Convenience Functions for Biscuit






A test harness for bsseq loading of Biscuit output, summarization of WGBS data over defined regions and in mappable samples, with or without imputation, dropping of mostly-NA rows, age estimates, etc.

package bioconductor-biscuiteer

(downloads) docker_bioconductor-biscuiteer



depends bioconductor-biobase:


depends bioconductor-biocgenerics:


depends bioconductor-biocparallel:


depends bioconductor-biscuiteerdata:


depends bioconductor-bsseq:


depends bioconductor-delayedmatrixstats:


depends bioconductor-dmrseq:


depends bioconductor-genomeinfodb:


depends bioconductor-genomicranges:


depends bioconductor-hdf5array:


depends bioconductor-homo.sapiens:


depends bioconductor-impute:


depends bioconductor-iranges:


depends bioconductor-mus.musculus:


depends bioconductor-qdnaseq:


depends bioconductor-rsamtools:


depends bioconductor-rtracklayer:


depends bioconductor-s4vectors:


depends bioconductor-summarizedexperiment:


depends bioconductor-variantannotation:


depends r-base:


depends r-data.table:

depends r-gtools:

depends r-matrix:

depends r-matrixstats:

depends r-qualv:

depends r-r.utils:

depends r-readr:



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-biscuiteer

and update with::

   mamba update bioconductor-biscuiteer

To create a new environment, run:

mamba create --name myenvname bioconductor-biscuiteer

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `bioconductor-biscuiteer/tags`_ for valid values for ``<tag>``)

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