recipe bioconductor-fcscan

fcScan for detecting clusters of coordinates with user defined options

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/fcScan.html

License:

Artistic-2.0

Recipe:

/bioconductor-fcscan/meta.yaml

This package is used to detect combination of genomic coordinates falling within a user defined window size along with user defined overlap between identified neighboring clusters. It can be used for genomic data where the clusters are built on a specific chromosome or specific strand. Clustering can be performed with a "greedy" option allowing thus the presence of additional sites within the allowed window size.

package bioconductor-fcscan

versions:

1.16.0-0,  1.14.0-0,  1.12.0-0,  1.8.0-0,  1.6.0-0,  1.4.0-1,  1.4.0-0,  1.2.0-0,  1.0.0-0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-rtracklayer:

>=1.62.0,<1.63.0

depends bioconductor-summarizedexperiment:

>=1.32.0,<1.33.0

depends bioconductor-variantannotation:

>=1.48.0,<1.49.0

depends r-base:

>=4.3,<4.4.0a0

depends r-doparallel:

depends r-foreach:

depends r-plyr:

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-fcscan

and update with::

   mamba update bioconductor-fcscan

To create a new environment, run:

mamba create --name myenvname bioconductor-fcscan

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 quay.io/biocontainers/bioconductor-fcscan:<tag>

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

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Link to this page

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