recipe bioconductor-tmixclust

Time Series Clustering of Gene Expression with Gaussian Mixed-Effects Models and Smoothing Splines

Homepage:

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

License:

GPL (>=2)

Recipe:

/bioconductor-tmixclust/meta.yaml

Implementation of a clustering method for time series gene expression data based on mixed-effects models with Gaussian variables and non-parametric cubic splines estimation. The method can robustly account for the high levels of noise present in typical gene expression time series datasets.

package bioconductor-tmixclust

versions:

1.28.0-0,  1.24.0-0,  1.22.0-0,  1.20.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.12.0-0,  1.10.0-0, 

1.28.0-0,  1.24.0-0,  1.22.0-0,  1.20.0-0,  1.16.0-0,  1.14.0-0,  1.12.0-1,  1.12.0-0,  1.10.0-0,  1.8.0-0,  1.6.0-1,  1.4.0-0

depends bioconductor-biobase:

>=2.66.0,<2.67.0

depends bioconductor-biocparallel:

>=1.40.0,<1.41.0

depends bioconductor-spem:

>=1.46.0,<1.47.0

depends r-base:

>=4.4,<4.5.0a0

depends r-cluster:

depends r-flexclust:

depends r-gss:

depends r-mvtnorm:

depends r-zoo:

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-tmixclust

and update with::

   mamba update bioconductor-tmixclust

To create a new environment, run:

mamba create --name myenvname bioconductor-tmixclust

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-tmixclust:<tag>

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

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Link to this page

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