recipe bioconductor-funchip

Clustering and Alignment of ChIP-Seq peaks based on their shapes

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-funchip/meta.yaml

Links:

biotools: funchip, doi: 10.1093/bioinformatics/btx201

Preprocessing and smoothing of ChIP-Seq peaks and efficient implementation of the k-mean alignment algorithm to classify them.

package bioconductor-funchip

versions:

1.28.0-0,  1.26.0-0,  1.24.0-1,  1.24.0-0,  1.20.0-2,  1.20.0-1,  1.20.0-0,  1.18.0-0,  1.16.0-1, 

1.28.0-0,  1.26.0-0,  1.24.0-1,  1.24.0-0,  1.20.0-2,  1.20.0-1,  1.20.0-0,  1.18.0-0,  1.16.0-1,  1.16.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.8.0-0,  1.6.0-0,  1.4.0-0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomeinfodb:

>=1.38.1,<1.39.0a0

depends bioconductor-genomicalignments:

>=1.38.0,<1.39.0

depends bioconductor-genomicalignments:

>=1.38.0,<1.39.0a0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-genomicranges:

>=1.54.1,<1.55.0a0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0a0

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-doparallel:

depends r-fda:

depends r-foreach:

depends r-rcolorbrewer:

depends r-rcpp:

depends r-shiny:

requirements:

additional platforms:

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-funchip

and update with::

   mamba update bioconductor-funchip

To create a new environment, run:

mamba create --name myenvname bioconductor-funchip

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-funchip:<tag>

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

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