recipe bioconductor-bsgenome.ggallus.ucsc.galgal3.masked

Full masked genome sequences for Gallus gallus (UCSC version galGal3)






Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal3, May 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Ggallus.UCSC.galGal3, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.

package bioconductor-bsgenome.ggallus.ucsc.galgal3.masked

(downloads) docker_bioconductor-bsgenome.ggallus.ucsc.galgal3.masked



depends bioconductor-bsgenome:


depends bioconductor-bsgenome.ggallus.ucsc.galgal3:


depends bioconductor-data-packages:


depends curl:

depends r-base:




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-bsgenome.ggallus.ucsc.galgal3.masked

and update with::

   mamba update bioconductor-bsgenome.ggallus.ucsc.galgal3.masked

To create a new environment, run:

mamba create --name myenvname bioconductor-bsgenome.ggallus.ucsc.galgal3.masked

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-bsgenome.ggallus.ucsc.galgal3.masked/tags`_ for valid values for ``<tag>``)

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