recipe bioconductor-frenchfish

Poisson Models for Quantifying DNA Copy-number from FISH Images of Tissue Sections

Homepage:

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

License:

Artistic-2.0

Recipe:

/bioconductor-frenchfish/meta.yaml

FrenchFISH comprises a nuclear volume correction method coupled with two types of Poisson models: either a Poisson model for improved manual spot counting without the need for control probes; or a homogenous Poisson Point Process model for automated spot counting.

package bioconductor-frenchfish

versions:

1.14.0-0,  1.12.0-0,  1.10.0-0,  1.6.0-0,  1.4.0-0,  1.2.0-1,  1.2.0-0,  1.0.0-0

depends r-base:

>=4.3,<4.4.0a0

depends r-mcmcpack:

depends r-nhpoisson:

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-frenchfish

and update with::

   mamba update bioconductor-frenchfish

To create a new environment, run:

mamba create --name myenvname bioconductor-frenchfish

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-frenchfish:<tag>

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

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