recipe bioconductor-mosaics

MOSAiCS (MOdel-based one and two Sample Analysis and Inference for ChIP-Seq)

Homepage:

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

License:

GPL (>= 2)

Recipe:

/bioconductor-mosaics/meta.yaml

Links:

biotools: mosaics, doi: 10.1198/jasa.2011.ap09706

This package provides functions for fitting MOSAiCS and MOSAiCS-HMM, a statistical framework to analyze one-sample or two-sample ChIP-seq data of transcription factor binding and histone modification.

package bioconductor-mosaics

versions:

2.40.0-0,  2.38.0-0,  2.36.0-0,  2.32.0-2,  2.32.0-1,  2.32.0-0,  2.30.0-0,  2.28.0-0,  2.26.0-0, 

2.40.0-0,  2.38.0-0,  2.36.0-0,  2.32.0-2,  2.32.0-1,  2.32.0-0,  2.30.0-0,  2.28.0-0,  2.26.0-0,  2.24.0-0,  2.22.0-1,  2.20.0-0,  2.18.0-0,  2.16.0-0,  2.14.0-0,  2.10.0-0,  2.4.1-0

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-iranges:

>=2.36.0,<2.37.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0a0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0a0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-s4vectors:

>=0.40.2,<0.41.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends perl:

>=5.32.1,<5.33.0a0 *_perl5

depends perl:

>=5.6.0

depends r-base:

>=4.3,<4.4.0a0

depends r-lattice:

depends r-mass:

depends r-rcpp:

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-mosaics

and update with::

   mamba update bioconductor-mosaics

To create a new environment, run:

mamba create --name myenvname bioconductor-mosaics

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-mosaics:<tag>

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

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[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-mosaics/README.html)